PL_MD_GROMACS.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "provenance": [],
      "collapsed_sections": [],
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    },
    "gpuClass": "standard"
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/avinashkarkada/GROMACS-COLAB/blob/main/PL_MD_GROMACS.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "_ZCBKwaRL6Ea",
        "outputId": "c988f190-01e8-429a-ddea-470d83dacad2"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Wed Aug 31 15:59:33 2022       \n",
            "+-----------------------------------------------------------------------------+\n",
            "| NVIDIA-SMI 460.32.03    Driver Version: 460.32.03    CUDA Version: 11.2     |\n",
            "|-------------------------------+----------------------+----------------------+\n",
            "| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |\n",
            "| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |\n",
            "|                               |                      |               MIG M. |\n",
            "|===============================+======================+======================|\n",
            "|   0  Tesla T4            Off  | 00000000:00:04.0 Off |                    0 |\n",
            "| N/A   47C    P8    10W /  70W |      0MiB / 15109MiB |      0%      Default |\n",
            "|                               |                      |                  N/A |\n",
            "+-------------------------------+----------------------+----------------------+\n",
            "                                                                               \n",
            "+-----------------------------------------------------------------------------+\n",
            "| Processes:                                                                  |\n",
            "|  GPU   GI   CI        PID   Type   Process name                  GPU Memory |\n",
            "|        ID   ID                                                   Usage      |\n",
            "|=============================================================================|\n",
            "|  No running processes found                                                 |\n",
            "+-----------------------------------------------------------------------------+\n"
          ]
        }
      ],
      "source": [
        "#@title Make sure you are connected to a GPU node\n",
        "\n",
        "gpu_info = !nvidia-smi\n",
        "gpu_info = '\\n'.join(gpu_info)\n",
        "if gpu_info.find('failed') >= 0:\n",
        "  print('Select the Runtime > \"Change runtime type\" menu to enable a GPU accelerator, ')\n",
        "  print('and then re-execute this cell.')\n",
        "else:\n",
        "  print(gpu_info)"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#@title Download and unzip the compressed folder of GROMACS 2020.6 version\n",
        "!wget https://raw.githubusercontent.com/pb3lab/ibm3202/master/software/gromacs.tar.gz\n",
        "!tar xzf gromacs.tar.gz"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "1Enpl2sFNqyD",
        "outputId": "77a482b4-d89b-4f75-8a35-38ac3e7a60ed"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "--2022-08-31 15:59:39--  https://raw.githubusercontent.com/pb3lab/ibm3202/master/software/gromacs.tar.gz\n",
            "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.110.133, ...\n",
            "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 35608971 (34M) [application/octet-stream]\n",
            "Saving to: ‘gromacs.tar.gz.1’\n",
            "\n",
            "gromacs.tar.gz.1    100%[===================>]  33.96M  --.-KB/s    in 0.09s   \n",
            "\n",
            "2022-08-31 15:59:42 (373 MB/s) - ‘gromacs.tar.gz.1’ saved [35608971/35608971]\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!pip install cmake --upgrade"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "bX3_dYR6Numw",
        "outputId": "e3c064a1-ab49-45af-d424-27d8cad06763"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/\n",
            "Requirement already satisfied: cmake in /usr/local/lib/python3.7/dist-packages (3.24.1)\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "%%bash\n",
        "source /content/gromacs/bin/GMXRC\n",
        "pwd\n",
        "gmx -h"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "2dwdeVWFNxCz",
        "outputId": "e0409d91-4fb0-46dd-843b-a41866be0053"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "/content\n",
            "SYNOPSIS\n",
            "\n",
            "gmx [-[no]h] [-[no]quiet] [-[no]version] [-[no]copyright] [-nice <int>]\n",
            "    [-[no]backup]\n",
            "\n",
            "OPTIONS\n",
            "\n",
            "Other options:\n",
            "\n",
            " -[no]h                     (no)\n",
            "           Print help and quit\n",
            " -[no]quiet                 (no)\n",
            "           Do not print common startup info or quotes\n",
            " -[no]version               (no)\n",
            "           Print extended version information and quit\n",
            " -[no]copyright             (yes)\n",
            "           Print copyright information on startup\n",
            " -nice   <int>              (19)\n",
            "           Set the nicelevel (default depends on command)\n",
            " -[no]backup                (yes)\n",
            "           Write backups if output files exist\n",
            "\n",
            "Additional help is available on the following topics:\n",
            "    commands    List of available commands\n",
            "    selections  Selection syntax and usage\n",
            "To access the help, use 'gmx help <topic>'.\n",
            "For help on a command, use 'gmx help <command>'.\n"
          ]
        },
        {
          "output_type": "stream",
          "name": "stderr",
          "text": [
            "                         :-) GROMACS - gmx, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content\n",
            "Command line:\n",
            "  gmx -h\n",
            "\n",
            "\n",
            "GROMACS reminds you: \"Look at these, my work-strong arms\" (P.J. Harvey)\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#@title Make a folder in google drive and enter its name. Paste the contents of your ligand.pdb, protein.pdb, complex.gro, all mdp files and forcefield folder.\n",
        "\n",
        "import os\n",
        "from pathlib import Path \n",
        "Folder_name = \"3htb\" #@param {type:\"string\"}\n",
        "mdpath = Path(\"/content/\" + Folder_name + \"/\") \n",
        "\n",
        "if os.path.exists(mdpath):\n",
        "  print(\"path already exists\")\n",
        "if not os.path.exists(mdpath):\n",
        "  os.mkdir(mdpath)\n",
        "  print(\"path was succesfully created\")\n",
        "\n",
        "os.chdir(mdpath)\n",
        "!pwd"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "FAJZEOP0N1et",
        "outputId": "0a950eac-976a-464e-e133-39b42240d6c9",
        "cellView": "form"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "path was succesfully created\n",
            "/content/3htb\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "from google.colab import drive\n",
        "import os\n",
        "from pathlib import Path\n",
        "\n",
        "drive.flush_and_unmount()\n",
        "drive.mount('/content/drive', force_remount=True)\n",
        "\n",
        "Google_Drive_Path = '/content/drive/MyDrive/prodrg-trial' #@param {type:\"string\"}\n",
        "workDir = Google_Drive_Path\n"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "o65dRpMyPdVs",
        "outputId": "1ea8afdf-1379-4b2b-aa76-535b1be6893b"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Mounted at /content/drive\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!cp -r $workDir/* $mdpath\n",
        "!pwd\n",
        "!chmod a+x *\n",
        "!ls -l"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "YH3a-tQgPgWi",
        "outputId": "61dda962-05d5-4c1e-b8db-1e10ccec872e"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "/content/3htb\n",
            "total 1240\n",
            "-rwx--x--x 1 root root  76800 Aug 31 16:00 complex.gro\n",
            "-rwx--x--x 1 root root   1061 Aug 31 16:00 em.mdp\n",
            "-rwx--x--x 1 root root   5992 Aug 31 16:00 FINAL_PL_both.sh\n",
            "drwx--x--x 2 root root   4096 Aug 31 16:00 gromos54a7_atb.ff\n",
            "-rwx--x--x 1 root root    922 Aug 31 16:00 ions.mdp\n",
            "-rwx--x--x 1 root root   1261 Aug 31 16:00 ligand_ATB.pdb\n",
            "-rwx--x--x 1 root root    534 Aug 31 16:00 ligand.gro\n",
            "-rwx--x--x 1 root root   6490 Aug 31 16:00 ligand.itp\n",
            "-rwx--x--x 1 root root    808 Aug 31 16:00 ligand.pdb\n",
            "-rwx--x--x 1 root root   2076 Aug 31 16:00 md.mdp\n",
            "-rwx--x--x 1 root root  10777 Aug 31 16:00 mdout.mdp\n",
            "-rwx--x--x 1 root root  76800 Aug 31 16:00 newbox.gro\n",
            "-rwx--x--x 1 root root   2088 Aug 31 16:00 npt.mdp\n",
            "-rwx--x--x 1 root root   1870 Aug 31 16:00 nvt.mdp\n",
            "-rwx--x--x 1 root root  40604 Aug 31 16:00 posre.itp\n",
            "-rwx--x--x 1 root root  40604 Aug 31 16:00 posre_Protein_chain_A.itp\n",
            "-rwx--x--x 1 root root  76350 Aug 31 16:00 protein.gro\n",
            "-rwx--x--x 1 root root 110538 Aug 31 16:00 protein.pdb\n",
            "-rwx--x--x 1 root root 384738 Aug 31 16:00 topol_Protein_chain_A.itp\n",
            "-rwx--x--x 1 root root 385240 Aug 31 16:00 topol.top\n",
            "-rwx--x--x 1 root root   1147 Aug 31 16:00 vacuum.mdp\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "%%bash\n",
        "source /content/gromacs/bin/GMXRC\n",
        "gmx editconf -f complex.gro -o newbox.gro -bt cubic -d 2.0 -c\n",
        "gmx grompp -f vacuum.mdp -c newbox.gro -p topol.top -o protein-EM-vacuum.tpr -maxwarn 200\n",
        "gmx mdrun -v -deffnm protein-EM-vacuum -c protein-EM-vacuum.pdb\n",
        "gmx mdrun -v -deffnm protein-EM-vacuum"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "cB9DjiGY-0Bz",
        "outputId": "f2a88b0b-8757-4b12-9fa8-3e83ea4d418b"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Note that major changes are planned in future for editconf, to improve usability and utility.\n",
            "Read 1705 atoms\n",
            "Volume: 85.2459 nm^3, corresponds to roughly 38300 electrons\n",
            "No velocities found\n",
            "    system size :  4.007  4.192  5.073 (nm)\n",
            "    diameter    :  5.849               (nm)\n",
            "    center      :  2.237 -1.666 -0.917 (nm)\n",
            "    box vectors :  4.008  4.193  5.073 (nm)\n",
            "    box angles  :  90.00  90.00  90.00 (degrees)\n",
            "    box volume  :  85.25               (nm^3)\n",
            "    shift       :  2.687  6.591  5.841 (nm)\n",
            "new center      :  4.925  4.925  4.925 (nm)\n",
            "new box vectors :  9.849  9.849  9.849 (nm)\n",
            "new box angles  :  90.00  90.00  90.00 (degrees)\n",
            "new box volume  : 955.44               (nm^3)\n",
            "\n",
            "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
            "J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof\n",
            "Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net\n",
            "Charge\n",
            "J. Chem. Theory Comput. 10 (2014) pp. 381-393\n",
            "-------- -------- --- Thank You --- -------- --------\n",
            "\n",
            "Analysing residue names:\n",
            "There are:   163    Protein residues\n",
            "There are:     1      Other residues\n",
            "Analysing Protein...\n",
            "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n",
            "Calculating fourier grid dimensions for X Y Z\n",
            "Using a fourier grid of 84x84x84, spacing 0.117 0.117 0.117\n",
            "This run will generate roughly 0 Mb of data\n"
          ]
        },
        {
          "output_type": "stream",
          "name": "stderr",
          "text": [
            "                     :-) GROMACS - gmx editconf, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx editconf, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx editconf -f complex.gro -o newbox.gro -bt cubic -d 2.0 -c\n",
            "\n",
            "\n",
            "Back Off! I just backed up newbox.gro to ./#newbox.gro.1#\n",
            "\n",
            "GROMACS reminds you: \"People who do QM/MM must be rather patient and enjoy quality over speed\" (Kresten Lindorff-Larsen)\n",
            "\n",
            "                      :-) GROMACS - gmx grompp, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx grompp, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx grompp -f vacuum.mdp -c newbox.gro -p topol.top -o protein-EM-vacuum.tpr -maxwarn 200\n",
            "\n",
            "Ignoring obsolete mdp entry 'title'\n",
            "Ignoring obsolete mdp entry 'ns_type'\n",
            "\n",
            "NOTE 1 [file vacuum.mdp]:\n",
            "  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note\n",
            "  that with the Verlet scheme, nstlist has no effect on the accuracy of\n",
            "  your simulation.\n",
            "\n",
            "Setting the LD random seed to -13701313\n",
            "Generated 210 of the 2556 non-bonded parameter combinations\n",
            "Excluding 3 bonded neighbours molecule type 'Protein_chain_A'\n",
            "Excluding 3 bonded neighbours molecule type 'JZ4'\n",
            "\n",
            "WARNING 1 [file topol.top, line 11007]:\n",
            "  The GROMOS force fields have been parametrized with a physically\n",
            "  incorrect multiple-time-stepping scheme for a twin-range cut-off. When\n",
            "  used with a single-range cut-off (or a correct Trotter\n",
            "  multiple-time-stepping scheme), physical properties, such as the density,\n",
            "  might differ from the intended values. Since there are researchers\n",
            "  actively working on validating GROMOS with modern integrators we have not\n",
            "  yet removed the GROMOS force fields, but you should be aware of these\n",
            "  issues and check if molecules in your system are affected before\n",
            "  proceeding. Further information is available at\n",
            "  https://redmine.gromacs.org/issues/2884 , and a longer explanation of our\n",
            "  decision to remove physically incorrect algorithms can be found at\n",
            "  https://doi.org/10.26434/chemrxiv.11474583.v1 .\n",
            "\n",
            "\n",
            "NOTE 2 [file topol.top, line 11007]:\n",
            "  System has non-zero total charge: 6.000000\n",
            "  Total charge should normally be an integer. See\n",
            "  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic\n",
            "  for discussion on how close it should be to an integer.\n",
            "  \n",
            "\n",
            "\n",
            "\n",
            "WARNING 2 [file topol.top, line 11007]:\n",
            "  You are using Ewald electrostatics in a system with net charge. This can\n",
            "  lead to severe artifacts, such as ions moving into regions with low\n",
            "  dielectric, due to the uniform background charge. We suggest to\n",
            "  neutralize your system with counter ions, possibly in combination with a\n",
            "  physiological salt concentration.\n",
            "\n",
            "Number of degrees of freedom in T-Coupling group rest is 5112.00\n",
            "Estimate for the relative computational load of the PME mesh part: 0.92\n",
            "\n",
            "NOTE 3 [file vacuum.mdp]:\n",
            "  The optimal PME mesh load for parallel simulations is below 0.5\n",
            "  and for highly parallel simulations between 0.25 and 0.33,\n",
            "  for higher performance, increase the cut-off and the PME grid spacing.\n",
            "\n",
            "\n",
            "\n",
            "There were 3 notes\n",
            "\n",
            "There were 2 warnings\n",
            "\n",
            "GROMACS reminds you: \"People who do QM/MM must be rather patient and enjoy quality over speed\" (Kresten Lindorff-Larsen)\n",
            "\n",
            "                      :-) GROMACS - gmx mdrun, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx mdrun, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx mdrun -v -deffnm protein-EM-vacuum -c protein-EM-vacuum.pdb\n",
            "\n",
            "Reading file protein-EM-vacuum.tpr, VERSION 2020.6 (single precision)\n",
            "1 GPU selected for this run.\n",
            "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
            "  PP:0\n",
            "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
            "PP task will update and constrain coordinates on the CPU\n",
            "Using 1 MPI thread\n",
            "\n",
            "Non-default thread affinity set, disabling internal thread affinity\n",
            "\n",
            "Using 2 OpenMP threads \n",
            "\n",
            "\n",
            "Steepest Descents:\n",
            "   Tolerance (Fmax)   =  1.00000e+03\n",
            "   Number of steps    =        50000\n",
            "Step=    0, Dmax= 1.0e-02 nm, Epot= -1.02542e+04 Fmax= 3.00987e+04, atom= 1703\n",
            "Step=    1, Dmax= 1.0e-02 nm, Epot= -1.20611e+04 Fmax= 1.27958e+04, atom= 1703\n",
            "Step=    2, Dmax= 1.2e-02 nm, Epot= -1.37941e+04 Fmax= 4.40797e+03, atom= 976\n",
            "Step=    3, Dmax= 1.4e-02 nm, Epot= -1.45711e+04 Fmax= 6.52054e+03, atom= 1704\n",
            "Step=    4, Dmax= 1.7e-02 nm, Epot= -1.42359e+04 Fmax= 2.00349e+04, atom= 1704\rStep=    5, Dmax= 8.6e-03 nm, Epot= -1.49619e+04 Fmax= 7.24006e+03, atom= 1704\n",
            "Step=    6, Dmax= 1.0e-02 nm, Epot= -1.51049e+04 Fmax= 1.00083e+04, atom= 1704\n",
            "Step=    7, Dmax= 1.2e-02 nm, Epot= -1.52039e+04 Fmax= 1.17716e+04, atom= 1704\n",
            "Step=    8, Dmax= 1.5e-02 nm, Epot= -1.52890e+04 Fmax= 1.40771e+04, atom= 1704\n",
            "Step=    9, Dmax= 1.8e-02 nm, Epot= -1.52906e+04 Fmax= 1.66634e+04, atom= 1704\n",
            "Step=   10, Dmax= 2.1e-02 nm, Epot= -1.53322e+04 Fmax= 2.10436e+04, atom= 1704\n",
            "Step=   11, Dmax= 2.6e-02 nm, Epot= -1.52508e+04 Fmax= 2.18154e+04, atom= 1704\rStep=   12, Dmax= 1.3e-02 nm, Epot= -1.55873e+04 Fmax= 4.25092e+03, atom= 1704\n",
            "Step=   13, Dmax= 1.5e-02 nm, Epot= -1.54860e+04 Fmax= 2.54222e+04, atom= 1704\rStep=   14, Dmax= 7.7e-03 nm, Epot= -1.56497e+04 Fmax= 8.79661e+03, atom= 1704\n",
            "Step=   15, Dmax= 9.3e-03 nm, Epot= -1.57005e+04 Fmax= 8.24571e+03, atom= 1704\n",
            "Step=   16, Dmax= 1.1e-02 nm, Epot= -1.57240e+04 Fmax= 1.16386e+04, atom= 1704\n",
            "Step=   17, Dmax= 1.3e-02 nm, Epot= -1.57432e+04 Fmax= 1.24612e+04, atom= 1704\n",
            "Step=   18, Dmax= 1.6e-02 nm, Epot= -1.57464e+04 Fmax= 1.65494e+04, atom= 1704\n",
            "Step=   19, Dmax= 1.9e-02 nm, Epot= -1.57204e+04 Fmax= 1.72487e+04, atom= 1704\rStep=   20, Dmax= 9.6e-03 nm, Epot= -1.59062e+04 Fmax= 2.59145e+03, atom= 1704\n",
            "Step=   21, Dmax= 1.2e-02 nm, Epot= -1.58903e+04 Fmax= 1.86456e+04, atom= 1704\rStep=   22, Dmax= 5.8e-03 nm, Epot= -1.59566e+04 Fmax= 7.12601e+03, atom= 1704\n",
            "Step=   23, Dmax= 6.9e-03 nm, Epot= -1.59944e+04 Fmax= 5.93395e+03, atom= 1704\n",
            "Step=   24, Dmax= 8.3e-03 nm, Epot= -1.60091e+04 Fmax= 9.13701e+03, atom= 1704\n",
            "Step=   25, Dmax= 1.0e-02 nm, Epot= -1.60319e+04 Fmax= 9.36729e+03, atom= 1704\n",
            "Step=   26, Dmax= 1.2e-02 nm, Epot= -1.60338e+04 Fmax= 1.26492e+04, atom= 1704\n",
            "Step=   27, Dmax= 1.4e-02 nm, Epot= -1.60301e+04 Fmax= 1.34343e+04, atom= 1704\rStep=   28, Dmax= 7.2e-03 nm, Epot= -1.61317e+04 Fmax= 1.69181e+03, atom= 1704\n",
            "Step=   29, Dmax= 8.6e-03 nm, Epot= -1.61676e+04 Fmax= 1.33799e+04, atom= 1704\n",
            "Step=   30, Dmax= 1.0e-02 nm, Epot= -1.62455e+04 Fmax= 6.82677e+03, atom= 1704\n",
            "Step=   31, Dmax= 1.2e-02 nm, Epot= -1.61600e+04 Fmax= 1.73870e+04, atom= 1704\rStep=   32, Dmax= 6.2e-03 nm, Epot= -1.62798e+04 Fmax= 4.47295e+03, atom= 1703\n",
            "Step=   33, Dmax= 7.5e-03 nm, Epot= -1.62735e+04 Fmax= 9.17463e+03, atom= 1704\rStep=   34, Dmax= 3.7e-03 nm, Epot= -1.63040e+04 Fmax= 2.75040e+03, atom= 1704\n",
            "Step=   35, Dmax= 4.5e-03 nm, Epot= -1.63240e+04 Fmax= 5.32116e+03, atom= 1703\n",
            "Step=   36, Dmax= 5.4e-03 nm, Epot= -1.63453e+04 Fmax= 4.93346e+03, atom= 1704\n",
            "Step=   37, Dmax= 6.4e-03 nm, Epot= -1.63563e+04 Fmax= 6.99857e+03, atom= 1704\n",
            "Step=   38, Dmax= 7.7e-03 nm, Epot= -1.63693e+04 Fmax= 7.54857e+03, atom= 1704\n",
            "Step=   39, Dmax= 9.3e-03 nm, Epot= -1.63731e+04 Fmax= 9.80964e+03, atom= 1704\n",
            "Step=   40, Dmax= 1.1e-02 nm, Epot= -1.63709e+04 Fmax= 1.08153e+04, atom= 1704\rStep=   41, Dmax= 5.6e-03 nm, Epot= -1.64334e+04 Fmax= 1.31133e+03, atom= 1704\n",
            "Step=   42, Dmax= 6.7e-03 nm, Epot= -1.64637e+04 Fmax= 1.04108e+04, atom= 1704\n",
            "Step=   43, Dmax= 8.0e-03 nm, Epot= -1.65147e+04 Fmax= 5.23483e+03, atom= 1704\n",
            "Step=   44, Dmax= 9.6e-03 nm, Epot= -1.64647e+04 Fmax= 1.35449e+04, atom= 1704\rStep=   45, Dmax= 4.8e-03 nm, Epot= -1.65366e+04 Fmax= 3.67499e+03, atom= 1703\n",
            "Step=   46, Dmax= 5.8e-03 nm, Epot= -1.65377e+04 Fmax= 7.06601e+03, atom= 1704\n",
            "Step=   47, Dmax= 6.9e-03 nm, Epot= -1.65628e+04 Fmax= 5.77534e+03, atom= 1704\n",
            "Step=   48, Dmax= 8.3e-03 nm, Epot= -1.65451e+04 Fmax= 9.59062e+03, atom= 1704\rStep=   49, Dmax= 4.2e-03 nm, Epot= -1.65887e+04 Fmax= 2.35176e+03, atom= 1704\n",
            "Step=   50, Dmax= 5.0e-03 nm, Epot= -1.65952e+04 Fmax= 6.94423e+03, atom= 1704\n",
            "Step=   51, Dmax= 6.0e-03 nm, Epot= -1.66208e+04 Fmax= 4.59354e+03, atom= 1704\n",
            "Step=   52, Dmax= 7.2e-03 nm, Epot= -1.66094e+04 Fmax= 9.13880e+03, atom= 1704\rStep=   53, Dmax= 3.6e-03 nm, Epot= -1.66409e+04 Fmax= 2.02531e+03, atom= 1703\n",
            "Step=   54, Dmax= 4.3e-03 nm, Epot= -1.66498e+04 Fmax= 6.01602e+03, atom= 1704\n",
            "Step=   55, Dmax= 5.2e-03 nm, Epot= -1.66750e+04 Fmax= 3.57989e+03, atom= 1703\n",
            "Step=   56, Dmax= 6.2e-03 nm, Epot= -1.66661e+04 Fmax= 7.90598e+03, atom= 1704\rStep=   57, Dmax= 3.1e-03 nm, Epot= -1.66899e+04 Fmax= 2.43300e+03, atom= 1704\n",
            "Step=   58, Dmax= 3.7e-03 nm, Epot= -1.67009e+04 Fmax= 4.50610e+03, atom= 1703\n",
            "Step=   59, Dmax= 4.5e-03 nm, Epot= -1.67148e+04 Fmax= 4.06052e+03, atom= 1704\n",
            "Step=   60, Dmax= 5.4e-03 nm, Epot= -1.67199e+04 Fmax= 6.07722e+03, atom= 1704\n",
            "Step=   61, Dmax= 6.4e-03 nm, Epot= -1.67303e+04 Fmax= 6.14340e+03, atom= 1704\n",
            "Step=   62, Dmax= 7.7e-03 nm, Epot= -1.67279e+04 Fmax= 8.56521e+03, atom= 1704\rStep=   63, Dmax= 3.9e-03 nm, Epot= -1.67594e+04 Fmax= 9.18946e+02, atom= 1703\n",
            "\n",
            "writing lowest energy coordinates.\n",
            "\n",
            "Steepest Descents converged to Fmax < 1000 in 64 steps\n",
            "Potential Energy  = -1.6759400e+04\n",
            "Maximum force     =  9.1894629e+02 on atom 1703\n",
            "Norm of force     =  8.8976180e+01\n",
            "\n",
            "GROMACS reminds you: \"I hadn't been aware that there were doors closed to me until I started knocking on them.\" (Gertrude Elion)\n",
            "\n",
            "                      :-) GROMACS - gmx mdrun, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx mdrun, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx mdrun -v -deffnm protein-EM-vacuum\n",
            "\n",
            "\n",
            "Back Off! I just backed up protein-EM-vacuum.log to ./#protein-EM-vacuum.log.1#\n",
            "Reading file protein-EM-vacuum.tpr, VERSION 2020.6 (single precision)\n",
            "1 GPU selected for this run.\n",
            "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
            "  PP:0\n",
            "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
            "PP task will update and constrain coordinates on the CPU\n",
            "Using 1 MPI thread\n",
            "\n",
            "Non-default thread affinity set, disabling internal thread affinity\n",
            "\n",
            "Using 2 OpenMP threads \n",
            "\n",
            "\n",
            "Back Off! I just backed up protein-EM-vacuum.trr to ./#protein-EM-vacuum.trr.1#\n",
            "\n",
            "Back Off! I just backed up protein-EM-vacuum.edr to ./#protein-EM-vacuum.edr.1#\n",
            "\n",
            "Steepest Descents:\n",
            "   Tolerance (Fmax)   =  1.00000e+03\n",
            "   Number of steps    =        50000\n",
            "Step=    0, Dmax= 1.0e-02 nm, Epot= -1.02542e+04 Fmax= 3.00987e+04, atom= 1703\n",
            "Step=    1, Dmax= 1.0e-02 nm, Epot= -1.20610e+04 Fmax= 1.27958e+04, atom= 1703\n",
            "Step=    2, Dmax= 1.2e-02 nm, Epot= -1.37941e+04 Fmax= 4.40797e+03, atom= 976\n",
            "Step=    3, Dmax= 1.4e-02 nm, Epot= -1.45711e+04 Fmax= 6.52054e+03, atom= 1704\n",
            "Step=    4, Dmax= 1.7e-02 nm, Epot= -1.42359e+04 Fmax= 2.00349e+04, atom= 1704\rStep=    5, Dmax= 8.6e-03 nm, Epot= -1.49619e+04 Fmax= 7.24006e+03, atom= 1704\n",
            "Step=    6, Dmax= 1.0e-02 nm, Epot= -1.51049e+04 Fmax= 1.00083e+04, atom= 1704\n",
            "Step=    7, Dmax= 1.2e-02 nm, Epot= -1.52039e+04 Fmax= 1.17716e+04, atom= 1704\n",
            "Step=    8, Dmax= 1.5e-02 nm, Epot= -1.52890e+04 Fmax= 1.40771e+04, atom= 1704\n",
            "Step=    9, Dmax= 1.8e-02 nm, Epot= -1.52906e+04 Fmax= 1.66634e+04, atom= 1704\n",
            "Step=   10, Dmax= 2.1e-02 nm, Epot= -1.53322e+04 Fmax= 2.10436e+04, atom= 1704\n",
            "Step=   11, Dmax= 2.6e-02 nm, Epot= -1.52508e+04 Fmax= 2.18154e+04, atom= 1704\rStep=   12, Dmax= 1.3e-02 nm, Epot= -1.55873e+04 Fmax= 4.25092e+03, atom= 1704\n",
            "Step=   13, Dmax= 1.5e-02 nm, Epot= -1.54860e+04 Fmax= 2.54222e+04, atom= 1704\rStep=   14, Dmax= 7.7e-03 nm, Epot= -1.56497e+04 Fmax= 8.79661e+03, atom= 1704\n",
            "Step=   15, Dmax= 9.3e-03 nm, Epot= -1.57005e+04 Fmax= 8.24571e+03, atom= 1704\n",
            "Step=   16, Dmax= 1.1e-02 nm, Epot= -1.57240e+04 Fmax= 1.16386e+04, atom= 1704\n",
            "Step=   17, Dmax= 1.3e-02 nm, Epot= -1.57432e+04 Fmax= 1.24612e+04, atom= 1704\n",
            "Step=   18, Dmax= 1.6e-02 nm, Epot= -1.57464e+04 Fmax= 1.65494e+04, atom= 1704\n",
            "Step=   19, Dmax= 1.9e-02 nm, Epot= -1.57204e+04 Fmax= 1.72487e+04, atom= 1704\rStep=   20, Dmax= 9.6e-03 nm, Epot= -1.59062e+04 Fmax= 2.59145e+03, atom= 1704\n",
            "Step=   21, Dmax= 1.2e-02 nm, Epot= -1.58903e+04 Fmax= 1.86456e+04, atom= 1704\rStep=   22, Dmax= 5.8e-03 nm, Epot= -1.59566e+04 Fmax= 7.12601e+03, atom= 1704\n",
            "Step=   23, Dmax= 6.9e-03 nm, Epot= -1.59944e+04 Fmax= 5.93395e+03, atom= 1704\n",
            "Step=   24, Dmax= 8.3e-03 nm, Epot= -1.60091e+04 Fmax= 9.13701e+03, atom= 1704\n",
            "Step=   25, Dmax= 1.0e-02 nm, Epot= -1.60319e+04 Fmax= 9.36729e+03, atom= 1704\n",
            "Step=   26, Dmax= 1.2e-02 nm, Epot= -1.60338e+04 Fmax= 1.26492e+04, atom= 1704\n",
            "Step=   27, Dmax= 1.4e-02 nm, Epot= -1.60301e+04 Fmax= 1.34343e+04, atom= 1704\rStep=   28, Dmax= 7.2e-03 nm, Epot= -1.61317e+04 Fmax= 1.69181e+03, atom= 1704\n",
            "Step=   29, Dmax= 8.6e-03 nm, Epot= -1.61676e+04 Fmax= 1.33799e+04, atom= 1704\n",
            "Step=   30, Dmax= 1.0e-02 nm, Epot= -1.62455e+04 Fmax= 6.82677e+03, atom= 1704\n",
            "Step=   31, Dmax= 1.2e-02 nm, Epot= -1.61600e+04 Fmax= 1.73870e+04, atom= 1704\rStep=   32, Dmax= 6.2e-03 nm, Epot= -1.62798e+04 Fmax= 4.47295e+03, atom= 1703\n",
            "Step=   33, Dmax= 7.5e-03 nm, Epot= -1.62735e+04 Fmax= 9.17463e+03, atom= 1704\rStep=   34, Dmax= 3.7e-03 nm, Epot= -1.63040e+04 Fmax= 2.75040e+03, atom= 1704\n",
            "Step=   35, Dmax= 4.5e-03 nm, Epot= -1.63240e+04 Fmax= 5.32116e+03, atom= 1703\n",
            "Step=   36, Dmax= 5.4e-03 nm, Epot= -1.63453e+04 Fmax= 4.93345e+03, atom= 1704\n",
            "Step=   37, Dmax= 6.4e-03 nm, Epot= -1.63563e+04 Fmax= 6.99857e+03, atom= 1704\n",
            "Step=   38, Dmax= 7.7e-03 nm, Epot= -1.63693e+04 Fmax= 7.54857e+03, atom= 1704\n",
            "Step=   39, Dmax= 9.3e-03 nm, Epot= -1.63731e+04 Fmax= 9.80964e+03, atom= 1704\n",
            "Step=   40, Dmax= 1.1e-02 nm, Epot= -1.63709e+04 Fmax= 1.08153e+04, atom= 1704\rStep=   41, Dmax= 5.6e-03 nm, Epot= -1.64334e+04 Fmax= 1.31133e+03, atom= 1704\n",
            "Step=   42, Dmax= 6.7e-03 nm, Epot= -1.64637e+04 Fmax= 1.04108e+04, atom= 1704\n",
            "Step=   43, Dmax= 8.0e-03 nm, Epot= -1.65147e+04 Fmax= 5.23483e+03, atom= 1704\n",
            "Step=   44, Dmax= 9.6e-03 nm, Epot= -1.64646e+04 Fmax= 1.35449e+04, atom= 1704\rStep=   45, Dmax= 4.8e-03 nm, Epot= -1.65366e+04 Fmax= 3.67499e+03, atom= 1703\n",
            "Step=   46, Dmax= 5.8e-03 nm, Epot= -1.65377e+04 Fmax= 7.06601e+03, atom= 1704\n",
            "Step=   47, Dmax= 6.9e-03 nm, Epot= -1.65628e+04 Fmax= 5.77535e+03, atom= 1704\n",
            "Step=   48, Dmax= 8.3e-03 nm, Epot= -1.65451e+04 Fmax= 9.59062e+03, atom= 1704\rStep=   49, Dmax= 4.2e-03 nm, Epot= -1.65887e+04 Fmax= 2.35176e+03, atom= 1704\n",
            "Step=   50, Dmax= 5.0e-03 nm, Epot= -1.65952e+04 Fmax= 6.94423e+03, atom= 1704\n",
            "Step=   51, Dmax= 6.0e-03 nm, Epot= -1.66208e+04 Fmax= 4.59354e+03, atom= 1704\n",
            "Step=   52, Dmax= 7.2e-03 nm, Epot= -1.66094e+04 Fmax= 9.13880e+03, atom= 1704\rStep=   53, Dmax= 3.6e-03 nm, Epot= -1.66409e+04 Fmax= 2.02530e+03, atom= 1703\n",
            "Step=   54, Dmax= 4.3e-03 nm, Epot= -1.66498e+04 Fmax= 6.01602e+03, atom= 1704\n",
            "Step=   55, Dmax= 5.2e-03 nm, Epot= -1.66750e+04 Fmax= 3.57975e+03, atom= 1703\n",
            "Step=   56, Dmax= 6.2e-03 nm, Epot= -1.66661e+04 Fmax= 7.90632e+03, atom= 1704\rStep=   57, Dmax= 3.1e-03 nm, Epot= -1.66899e+04 Fmax= 2.43322e+03, atom= 1704\n",
            "Step=   58, Dmax= 3.7e-03 nm, Epot= -1.67009e+04 Fmax= 4.50610e+03, atom= 1703\n",
            "Step=   59, Dmax= 4.5e-03 nm, Epot= -1.67148e+04 Fmax= 4.06052e+03, atom= 1704\n",
            "Step=   60, Dmax= 5.4e-03 nm, Epot= -1.67198e+04 Fmax= 6.07722e+03, atom= 1704\n",
            "Step=   61, Dmax= 6.4e-03 nm, Epot= -1.67303e+04 Fmax= 6.14340e+03, atom= 1704\n",
            "Step=   62, Dmax= 7.7e-03 nm, Epot= -1.67278e+04 Fmax= 8.56521e+03, atom= 1704\rStep=   63, Dmax= 3.9e-03 nm, Epot= -1.67594e+04 Fmax= 9.18946e+02, atom= 1703\n",
            "\n",
            "writing lowest energy coordinates.\n",
            "\n",
            "Steepest Descents converged to Fmax < 1000 in 64 steps\n",
            "Potential Energy  = -1.6759404e+04\n",
            "Maximum force     =  9.1894580e+02 on atom 1703\n",
            "Norm of force     =  8.8976363e+01\n",
            "\n",
            "GROMACS reminds you: \"Documentation is like sex: When it's good it's great, and when it's bad it's better than nothing.\" (Linus Torvalds)\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "%%bash\n",
        "source /content/gromacs/bin/GMXRC\n",
        "gmx solvate -cp protein-EM-vacuum.gro -cs spc216.gro -p topol.top -o solv.gro\n",
        "gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 2\n",
        "gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -conc 0.15  -neutral -pname NA -nname CL <<< 15\n",
        "gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr -maxwarn 2\n",
        "gmx mdrun -v -deffnm em"
      ],
      "metadata": {
        "id": "EdB3S0Kw-9OS",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "896f60a7-180b-478d-c7d7-4549f58c2f5d"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "\n",
            "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n",
            "         based on residue and atom names, since they could not be\n",
            "         definitively assigned from the information in your input\n",
            "         files. These guessed numbers might deviate from the mass\n",
            "         and radius of the atom type. Please check the output\n",
            "         files if necessary.\n",
            "\n",
            "NOTE: From version 5.0 gmx solvate uses the Van der Waals radii\n",
            "from the source below. This means the results may be different\n",
            "compared to previous GROMACS versions.\n",
            "\n",
            "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
            "A. Bondi\n",
            "van der Waals Volumes and Radii\n",
            "J. Phys. Chem. 68 (1964) pp. 441-451\n",
            "-------- -------- --- Thank You --- -------- --------\n",
            "\n",
            "Adding line for 30862 solvent molecules with resname (SOL) to topology file (topol.top)\n",
            "\n",
            "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
            "J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof\n",
            "Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net\n",
            "Charge\n",
            "J. Chem. Theory Comput. 10 (2014) pp. 381-393\n",
            "-------- -------- --- Thank You --- -------- --------\n",
            "\n",
            "Analysing residue names:\n",
            "There are:   163    Protein residues\n",
            "There are:     1      Other residues\n",
            "There are: 30862      Water residues\n",
            "Analysing Protein...\n",
            "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n",
            "Calculating fourier grid dimensions for X Y Z\n",
            "Using a fourier grid of 84x84x84, spacing 0.117 0.117 0.117\n",
            "This run will generate roughly 7 Mb of data\n",
            "Will try to add 86 NA ions and 92 CL ions.\n",
            "Select a continuous group of solvent molecules\n",
            "Selected 15: 'SOL'\n",
            "\n",
            "Processing topology\n",
            "Replacing 178 solute molecules in topology file (topol.top)  by 86 NA and 92 CL ions.\n",
            "Analysing residue names:\n",
            "There are:   163    Protein residues\n",
            "There are:     1      Other residues\n",
            "There are: 30684      Water residues\n",
            "There are:   178        Ion residues\n",
            "Analysing Protein...\n",
            "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n",
            "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n",
            "Calculating fourier grid dimensions for X Y Z\n",
            "Using a fourier grid of 84x84x84, spacing 0.117 0.117 0.117\n",
            "This run will generate roughly 7 Mb of data\n"
          ]
        },
        {
          "output_type": "stream",
          "name": "stderr",
          "text": [
            "                     :-) GROMACS - gmx solvate, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx solvate, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx solvate -cp protein-EM-vacuum.gro -cs spc216.gro -p topol.top -o solv.gro\n",
            "\n",
            "Reading solute configuration\n",
            "Reading solvent configuration\n",
            "\n",
            "Initialising inter-atomic distances...\n",
            "Generating solvent configuration\n",
            "Will generate new solvent configuration of 6x6x6 boxes\n",
            "Solvent box contains 104712 atoms in 34904 residues\n",
            "Removed 9879 solvent atoms due to solvent-solvent overlap\n",
            "Removed 2247 solvent atoms due to solute-solvent overlap\n",
            "Sorting configuration\n",
            "Found 1 molecule type:\n",
            "    SOL (   3 atoms): 30862 residues\n",
            "Generated solvent containing 92586 atoms in 30862 residues\n",
            "Writing generated configuration to solv.gro\n",
            "\n",
            "Output configuration contains 94291 atoms in 31026 residues\n",
            "Volume                 :     955.439 (nm^3)\n",
            "Density                :     999.341 (g/l)\n",
            "Number of solvent molecules:  30862   \n",
            "\n",
            "Processing topology\n",
            "\n",
            "Back Off! I just backed up topol.top to ./#topol.top.1#\n",
            "\n",
            "GROMACS reminds you: \"Philosophy of science is about as useful to scientists as ornithology is to birds.\" (Richard Feynman)\n",
            "\n",
            "                      :-) GROMACS - gmx grompp, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx grompp, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 2\n",
            "\n",
            "Ignoring obsolete mdp entry 'title'\n",
            "Ignoring obsolete mdp entry 'ns_type'\n",
            "\n",
            "NOTE 1 [file em.mdp]:\n",
            "  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note\n",
            "  that with the Verlet scheme, nstlist has no effect on the accuracy of\n",
            "  your simulation.\n",
            "\n",
            "Setting the LD random seed to -295703234\n",
            "Generated 210 of the 2556 non-bonded parameter combinations\n",
            "Excluding 3 bonded neighbours molecule type 'Protein_chain_A'\n",
            "Excluding 3 bonded neighbours molecule type 'JZ4'\n",
            "Excluding 2 bonded neighbours molecule type 'SOL'\n",
            "\n",
            "WARNING 1 [file topol.top, line 11008]:\n",
            "  The GROMOS force fields have been parametrized with a physically\n",
            "  incorrect multiple-time-stepping scheme for a twin-range cut-off. When\n",
            "  used with a single-range cut-off (or a correct Trotter\n",
            "  multiple-time-stepping scheme), physical properties, such as the density,\n",
            "  might differ from the intended values. Since there are researchers\n",
            "  actively working on validating GROMOS with modern integrators we have not\n",
            "  yet removed the GROMOS force fields, but you should be aware of these\n",
            "  issues and check if molecules in your system are affected before\n",
            "  proceeding. Further information is available at\n",
            "  https://redmine.gromacs.org/issues/2884 , and a longer explanation of our\n",
            "  decision to remove physically incorrect algorithms can be found at\n",
            "  https://doi.org/10.26434/chemrxiv.11474583.v1 .\n",
            "\n",
            "\n",
            "NOTE 2 [file topol.top, line 11008]:\n",
            "  System has non-zero total charge: 6.000000\n",
            "  Total charge should normally be an integer. See\n",
            "  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic\n",
            "  for discussion on how close it should be to an integer.\n",
            "  \n",
            "\n",
            "\n",
            "\n",
            "WARNING 2 [file topol.top, line 11008]:\n",
            "  You are using Ewald electrostatics in a system with net charge. This can\n",
            "  lead to severe artifacts, such as ions moving into regions with low\n",
            "  dielectric, due to the uniform background charge. We suggest to\n",
            "  neutralize your system with counter ions, possibly in combination with a\n",
            "  physiological salt concentration.\n",
            "\n",
            "Number of degrees of freedom in T-Coupling group rest is 190284.00\n",
            "Estimate for the relative computational load of the PME mesh part: 0.26\n",
            "\n",
            "There were 2 notes\n",
            "\n",
            "There were 2 warnings\n",
            "\n",
            "GROMACS reminds you: \"Aristotle maintained that women have fewer teeth than men; although he was twice married, it never occurred to him to verify this statement by examining his wives' mouths.\" (Bertrand Russell)\n",
            "\n",
            "                      :-) GROMACS - gmx genion, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx genion, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -conc 0.15 -neutral -pname NA -nname CL\n",
            "\n",
            "Reading file ions.tpr, VERSION 2020.6 (single precision)\n",
            "Reading file ions.tpr, VERSION 2020.6 (single precision)\n",
            "Group     0 (         System) has 94291 elements\n",
            "Group     1 (        Protein) has  1695 elements\n",
            "Group     2 (      Protein-H) has  1301 elements\n",
            "Group     3 (        C-alpha) has   163 elements\n",
            "Group     4 (       Backbone) has   489 elements\n",
            "Group     5 (      MainChain) has   653 elements\n",
            "Group     6 (   MainChain+Cb) has   805 elements\n",
            "Group     7 (    MainChain+H) has   815 elements\n",
            "Group     8 (      SideChain) has   880 elements\n",
            "Group     9 (    SideChain-H) has   648 elements\n",
            "Group    10 (    Prot-Masses) has  1695 elements\n",
            "Group    11 (    non-Protein) has 92596 elements\n",
            "Group    12 (          Other) has    10 elements\n",
            "Group    13 (            JZ4) has    10 elements\n",
            "Group    14 (          Water) has 92586 elements\n",
            "Group    15 (            SOL) has 92586 elements\n",
            "Group    16 (      non-Water) has  1705 elements\n",
            "Select a group: Number of (3-atomic) solvent molecules: 30862\n",
            "\n",
            "Back Off! I just backed up topol.top to ./#topol.top.2#\n",
            "Using random seed 819287475.\n",
            "Replacing solvent molecule 29377 (atom 89836) with NA\n",
            "Replacing solvent molecule 6755 (atom 21970) with NA\n",
            "Replacing solvent molecule 5045 (atom 16840) with NA\n",
            "Replacing solvent molecule 27647 (atom 84646) with NA\n",
            "Replacing solvent molecule 969 (atom 4612) with NA\n",
            "Replacing solvent molecule 26176 (atom 80233) with NA\n",
            "Replacing solvent molecule 17997 (atom 55696) with NA\n",
            "Replacing solvent molecule 11888 (atom 37369) with NA\n",
            "Replacing solvent molecule 400 (atom 2905) with NA\n",
            "Replacing solvent molecule 30435 (atom 93010) with NA\n",
            "Replacing solvent molecule 1364 (atom 5797) with NA\n",
            "Replacing solvent molecule 16885 (atom 52360) with NA\n",
            "Replacing solvent molecule 30084 (atom 91957) with NA\n",
            "Replacing solvent molecule 18041 (atom 55828) with NA\n",
            "Replacing solvent molecule 19309 (atom 59632) with NA\n",
            "Replacing solvent molecule 20498 (atom 63199) with NA\n",
            "Replacing solvent molecule 11821 (atom 37168) with NA\n",
            "Replacing solvent molecule 4272 (atom 14521) with NA\n",
            "Replacing solvent molecule 5469 (atom 18112) with NA\n",
            "Replacing solvent molecule 8670 (atom 27715) with NA\n",
            "Replacing solvent molecule 27784 (atom 85057) with NA\n",
            "Replacing solvent molecule 23129 (atom 71092) with NA\n",
            "Replacing solvent molecule 18838 (atom 58219) with NA\n",
            "Replacing solvent molecule 19159 (atom 59182) with NA\n",
            "Replacing solvent molecule 7409 (atom 23932) with NA\n",
            "Replacing solvent molecule 16060 (atom 49885) with NA\n",
            "Replacing solvent molecule 3767 (atom 13006) with NA\n",
            "Replacing solvent molecule 21988 (atom 67669) with NA\n",
            "Replacing solvent molecule 25181 (atom 77248) with NA\n",
            "Replacing solvent molecule 8740 (atom 27925) with NA\n",
            "Replacing solvent molecule 21678 (atom 66739) with NA\n",
            "Replacing solvent molecule 18142 (atom 56131) with NA\n",
            "Replacing solvent molecule 18195 (atom 56290) with NA\n",
            "Replacing solvent molecule 885 (atom 4360) with NA\n",
            "Replacing solvent molecule 8609 (atom 27532) with NA\n",
            "Replacing solvent molecule 18915 (atom 58450) with NA\n",
            "Replacing solvent molecule 24174 (atom 74227) with NA\n",
            "Replacing solvent molecule 15125 (atom 47080) with NA\n",
            "Replacing solvent molecule 2799 (atom 10102) with NA\n",
            "Replacing solvent molecule 7634 (atom 24607) with NA\n",
            "Replacing solvent molecule 14710 (atom 45835) with NA\n",
            "Replacing solvent molecule 16017 (atom 49756) with NA\n",
            "Replacing solvent molecule 3866 (atom 13303) with NA\n",
            "Replacing solvent molecule 20031 (atom 61798) with NA\n",
            "Replacing solvent molecule 9822 (atom 31171) with NA\n",
            "Replacing solvent molecule 8480 (atom 27145) with NA\n",
            "Replacing solvent molecule 3059 (atom 10882) with NA\n",
            "Replacing solvent molecule 20228 (atom 62389) with NA\n",
            "Replacing solvent molecule 165 (atom 2200) with NA\n",
            "Replacing solvent molecule 18294 (atom 56587) with NA\n",
            "Replacing solvent molecule 3892 (atom 13381) with NA\n",
            "Replacing solvent molecule 19786 (atom 61063) with NA\n",
            "Replacing solvent molecule 8895 (atom 28390) with NA\n",
            "Replacing solvent molecule 15628 (atom 48589) with NA\n",
            "Replacing solvent molecule 1012 (atom 4741) with NA\n",
            "Replacing solvent molecule 11393 (atom 35884) with NA\n",
            "Replacing solvent molecule 10788 (atom 34069) with NA\n",
            "Replacing solvent molecule 957 (atom 4576) with NA\n",
            "Replacing solvent molecule 30738 (atom 93919) with NA\n",
            "Replacing solvent molecule 3116 (atom 11053) with NA\n",
            "Replacing solvent molecule 16860 (atom 52285) with NA\n",
            "Replacing solvent molecule 7112 (atom 23041) with NA\n",
            "Replacing solvent molecule 3949 (atom 13552) with NA\n",
            "Replacing solvent molecule 562 (atom 3391) with NA\n",
            "Replacing solvent molecule 5729 (atom 18892) with NA\n",
            "Replacing solvent molecule 29289 (atom 89572) with NA\n",
            "Replacing solvent molecule 6877 (atom 22336) with NA\n",
            "Replacing solvent molecule 5415 (atom 17950) with NA\n",
            "Replacing solvent molecule 23974 (atom 73627) with NA\n",
            "Replacing solvent molecule 18652 (atom 57661) with NA\n",
            "Replacing solvent molecule 25278 (atom 77539) with NA\n",
            "Replacing solvent molecule 7397 (atom 23896) with NA\n",
            "Replacing solvent molecule 5746 (atom 18943) with NA\n",
            "Replacing solvent molecule 14838 (atom 46219) with NA\n",
            "Replacing solvent molecule 18728 (atom 57889) with NA\n",
            "Replacing solvent molecule 15050 (atom 46855) with NA\n",
            "Replacing solvent molecule 23349 (atom 71752) with NA\n",
            "Replacing solvent molecule 10713 (atom 33844) with NA\n",
            "Replacing solvent molecule 25273 (atom 77524) with NA\n",
            "Replacing solvent molecule 21328 (atom 65689) with NA\n",
            "Replacing solvent molecule 3445 (atom 12040) with NA\n",
            "Replacing solvent molecule 4337 (atom 14716) with NA\n",
            "Replacing solvent molecule 6399 (atom 20902) with NA\n",
            "Replacing solvent molecule 29500 (atom 90205) with NA\n",
            "Replacing solvent molecule 20416 (atom 62953) with NA\n",
            "Replacing solvent molecule 12567 (atom 39406) with NA\n",
            "Replacing solvent molecule 490 (atom 3175) with CL\n",
            "Replacing solvent molecule 25381 (atom 77848) with CL\n",
            "Replacing solvent molecule 1638 (atom 6619) with CL\n",
            "Replacing solvent molecule 2026 (atom 7783) with CL\n",
            "Replacing solvent molecule 21952 (atom 67561) with CL\n",
            "Replacing solvent molecule 23009 (atom 70732) with CL\n",
            "Replacing solvent molecule 22848 (atom 70249) with CL\n",
            "Replacing solvent molecule 25838 (atom 79219) with CL\n",
            "Replacing solvent molecule 12019 (atom 37762) with CL\n",
            "Replacing solvent molecule 20631 (atom 63598) with CL\n",
            "Replacing solvent molecule 11039 (atom 34822) with CL\n",
            "Replacing solvent molecule 20340 (atom 62725) with CL\n",
            "Replacing solvent molecule 10005 (atom 31720) with CL\n",
            "Replacing solvent molecule 2790 (atom 10075) with CL\n",
            "Replacing solvent molecule 13630 (atom 42595) with CL\n",
            "Replacing solvent molecule 1807 (atom 7126) with CL\n",
            "Replacing solvent molecule 29865 (atom 91300) with CL\n",
            "Replacing solvent molecule 441 (atom 3028) with CL\n",
            "Replacing solvent molecule 22217 (atom 68356) with CL\n",
            "Replacing solvent molecule 5673 (atom 18724) with CL\n",
            "Replacing solvent molecule 14196 (atom 44293) with CL\n",
            "Replacing solvent molecule 18264 (atom 56497) with CL\n",
            "Replacing solvent molecule 17573 (atom 54424) with CL\n",
            "Replacing solvent molecule 27091 (atom 82978) with CL\n",
            "Replacing solvent molecule 24082 (atom 73951) with CL\n",
            "Replacing solvent molecule 7783 (atom 25054) with CL\n",
            "Replacing solvent molecule 9458 (atom 30079) with CL\n",
            "Replacing solvent molecule 28356 (atom 86773) with CL\n",
            "Replacing solvent molecule 29368 (atom 89809) with CL\n",
            "Replacing solvent molecule 22768 (atom 70009) with CL\n",
            "Replacing solvent molecule 22682 (atom 69751) with CL\n",
            "Replacing solvent molecule 7529 (atom 24292) with CL\n",
            "Replacing solvent molecule 7414 (atom 23947) with CL\n",
            "Replacing solvent molecule 27222 (atom 83371) with CL\n",
            "Replacing solvent molecule 27054 (atom 82867) with CL\n",
            "Replacing solvent molecule 1624 (atom 6577) with CL\n",
            "Replacing solvent molecule 24048 (atom 73849) with CL\n",
            "Replacing solvent molecule 23203 (atom 71314) with CL\n",
            "Replacing solvent molecule 53 (atom 1864) with CL\n",
            "Replacing solvent molecule 28186 (atom 86263) with CL\n",
            "Replacing solvent molecule 23843 (atom 73234) with CL\n",
            "Replacing solvent molecule 15740 (atom 48925) with CL\n",
            "Replacing solvent molecule 13417 (atom 41956) with CL\n",
            "Replacing solvent molecule 23404 (atom 71917) with CL\n",
            "Replacing solvent molecule 11589 (atom 36472) with CL\n",
            "Replacing solvent molecule 13811 (atom 43138) with CL\n",
            "Replacing solvent molecule 24035 (atom 73810) with CL\n",
            "Replacing solvent molecule 5766 (atom 19003) with CL\n",
            "Replacing solvent molecule 21216 (atom 65353) with CL\n",
            "Replacing solvent molecule 10453 (atom 33064) with CL\n",
            "Replacing solvent molecule 26503 (atom 81214) with CL\n",
            "Replacing solvent molecule 18506 (atom 57223) with CL\n",
            "Replacing solvent molecule 23560 (atom 72385) with CL\n",
            "Replacing solvent molecule 12960 (atom 40585) with CL\n",
            "Replacing solvent molecule 17030 (atom 52795) with CL\n",
            "Replacing solvent molecule 4160 (atom 14185) with CL\n",
            "Replacing solvent molecule 9092 (atom 28981) with CL\n",
            "Replacing solvent molecule 24706 (atom 75823) with CL\n",
            "Replacing solvent molecule 3393 (atom 11884) with CL\n",
            "Replacing solvent molecule 15893 (atom 49384) with CL\n",
            "Replacing solvent molecule 23137 (atom 71116) with CL\n",
            "Replacing solvent molecule 5056 (atom 16873) with CL\n",
            "Replacing solvent molecule 4846 (atom 16243) with CL\n",
            "Replacing solvent molecule 16430 (atom 50995) with CL\n",
            "Replacing solvent molecule 879 (atom 4342) with CL\n",
            "Replacing solvent molecule 776 (atom 4033) with CL\n",
            "Replacing solvent molecule 16277 (atom 50536) with CL\n",
            "Replacing solvent molecule 28429 (atom 86992) with CL\n",
            "Replacing solvent molecule 21734 (atom 66907) with CL\n",
            "Replacing solvent molecule 1134 (atom 5107) with CL\n",
            "Replacing solvent molecule 8440 (atom 27025) with CL\n",
            "Replacing solvent molecule 23758 (atom 72979) with CL\n",
            "Replacing solvent molecule 29263 (atom 89494) with CL\n",
            "Replacing solvent molecule 16103 (atom 50014) with CL\n",
            "Replacing solvent molecule 9716 (atom 30853) with CL\n",
            "Replacing solvent molecule 7790 (atom 25075) with CL\n",
            "Replacing solvent molecule 11866 (atom 37303) with CL\n",
            "Replacing solvent molecule 19831 (atom 61198) with CL\n",
            "Replacing solvent molecule 10118 (atom 32059) with CL\n",
            "Replacing solvent molecule 23962 (atom 73591) with CL\n",
            "Replacing solvent molecule 13942 (atom 43531) with CL\n",
            "Replacing solvent molecule 21979 (atom 67642) with CL\n",
            "Replacing solvent molecule 8244 (atom 26437) with CL\n",
            "Replacing solvent molecule 12352 (atom 38761) with CL\n",
            "Replacing solvent molecule 14074 (atom 43927) with CL\n",
            "Replacing solvent molecule 28295 (atom 86590) with CL\n",
            "Replacing solvent molecule 1602 (atom 6511) with CL\n",
            "Replacing solvent molecule 25272 (atom 77521) with CL\n",
            "Replacing solvent molecule 23279 (atom 71542) with CL\n",
            "Replacing solvent molecule 24915 (atom 76450) with CL\n",
            "Replacing solvent molecule 868 (atom 4309) with CL\n",
            "Replacing solvent molecule 18846 (atom 58243) with CL\n",
            "\n",
            "\n",
            "GROMACS reminds you: \"Aristotle maintained that women have fewer teeth than men; although he was twice married, it never occurred to him to verify this statement by examining his wives' mouths.\" (Bertrand Russell)\n",
            "\n",
            "                      :-) GROMACS - gmx grompp, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx grompp, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr -maxwarn 2\n",
            "\n",
            "Ignoring obsolete mdp entry 'title'\n",
            "Ignoring obsolete mdp entry 'ns_type'\n",
            "\n",
            "NOTE 1 [file em.mdp]:\n",
            "  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note\n",
            "  that with the Verlet scheme, nstlist has no effect on the accuracy of\n",
            "  your simulation.\n",
            "\n",
            "Setting the LD random seed to -65636\n",
            "Generated 210 of the 2556 non-bonded parameter combinations\n",
            "Excluding 3 bonded neighbours molecule type 'Protein_chain_A'\n",
            "Excluding 3 bonded neighbours molecule type 'JZ4'\n",
            "Excluding 2 bonded neighbours molecule type 'SOL'\n",
            "Excluding 1 bonded neighbours molecule type 'NA'\n",
            "Excluding 1 bonded neighbours molecule type 'CL'\n",
            "\n",
            "WARNING 1 [file topol.top, line 11010]:\n",
            "  The GROMOS force fields have been parametrized with a physically\n",
            "  incorrect multiple-time-stepping scheme for a twin-range cut-off. When\n",
            "  used with a single-range cut-off (or a correct Trotter\n",
            "  multiple-time-stepping scheme), physical properties, such as the density,\n",
            "  might differ from the intended values. Since there are researchers\n",
            "  actively working on validating GROMOS with modern integrators we have not\n",
            "  yet removed the GROMOS force fields, but you should be aware of these\n",
            "  issues and check if molecules in your system are affected before\n",
            "  proceeding. Further information is available at\n",
            "  https://redmine.gromacs.org/issues/2884 , and a longer explanation of our\n",
            "  decision to remove physically incorrect algorithms can be found at\n",
            "  https://doi.org/10.26434/chemrxiv.11474583.v1 .\n",
            "\n",
            "Number of degrees of freedom in T-Coupling group rest is 189750.00\n",
            "Estimate for the relative computational load of the PME mesh part: 0.27\n",
            "\n",
            "There was 1 note\n",
            "\n",
            "There was 1 warning\n",
            "\n",
            "GROMACS reminds you: \"Aristotle maintained that women have fewer teeth than men; although he was twice married, it never occurred to him to verify this statement by examining his wives' mouths.\" (Bertrand Russell)\n",
            "\n",
            "                      :-) GROMACS - gmx mdrun, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx mdrun, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx mdrun -v -deffnm em\n",
            "\n",
            "Reading file em.tpr, VERSION 2020.6 (single precision)\n",
            "1 GPU selected for this run.\n",
            "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
            "  PP:0\n",
            "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
            "PP task will update and constrain coordinates on the CPU\n",
            "Using 1 MPI thread\n",
            "\n",
            "Non-default thread affinity set, disabling internal thread affinity\n",
            "\n",
            "Using 2 OpenMP threads \n",
            "\n",
            "\n",
            "Steepest Descents:\n",
            "   Tolerance (Fmax)   =  1.00000e+03\n",
            "   Number of steps    =        50000\n",
            "Step=    0, Dmax= 2.0e-03 nm, Epot= -8.13753e+05 Fmax= 7.49365e+05, atom= 93849\n",
            "Step=    1, Dmax= 2.0e-03 nm, Epot= -8.28663e+05 Fmax= 5.69764e+05, atom= 93849\n",
            "Step=    2, Dmax= 2.4e-03 nm, Epot= -8.47560e+05 Fmax= 4.12150e+05, atom= 93849\n",
            "Step=    3, Dmax= 2.9e-03 nm, Epot= -8.71868e+05 Fmax= 2.92151e+05, atom= 226\n",
            "Step=    4, Dmax= 3.5e-03 nm, Epot= -9.02254e+05 Fmax= 2.17381e+05, atom= 1408\n",
            "Step=    5, Dmax= 4.1e-03 nm, Epot= -9.36582e+05 Fmax= 1.58770e+05, atom= 1408\n",
            "Step=    6, Dmax= 5.0e-03 nm, Epot= -9.74354e+05 Fmax= 1.10855e+05, atom= 1408\n",
            "Step=    7, Dmax= 6.0e-03 nm, Epot= -1.01559e+06 Fmax= 7.20591e+04, atom= 1408\n",
            "Step=    8, Dmax= 7.2e-03 nm, Epot= -1.06098e+06 Fmax= 4.31337e+04, atom= 1492\n",
            "Step=    9, Dmax= 8.6e-03 nm, Epot= -1.11102e+06 Fmax= 2.31788e+04, atom= 1492\n",
            "Step=   10, Dmax= 1.0e-02 nm, Epot= -1.16650e+06 Fmax= 1.41127e+04, atom= 61337\n",
            "Step=   11, Dmax= 1.2e-02 nm, Epot= -1.21690e+06 Fmax= 9.40771e+03, atom= 61337\n",
            "Step=   12, Dmax= 1.5e-02 nm, Epot= -1.26269e+06 Fmax= 5.83941e+03, atom= 61337\n",
            "Step=   13, Dmax= 1.8e-02 nm, Epot= -1.31239e+06 Fmax= 3.83513e+03, atom= 1492\n",
            "Step=   14, Dmax= 2.1e-02 nm, Epot= -1.36423e+06 Fmax= 1.23671e+04, atom= 1703\n",
            "Step=   15, Dmax= 2.6e-02 nm, Epot= -1.37561e+06 Fmax= 4.39474e+04, atom= 1703\n",
            "Step=   16, Dmax= 3.1e-02 nm, Epot= -1.38102e+06 Fmax= 1.72660e+04, atom= 1704\n",
            "Step=   17, Dmax= 3.7e-02 nm, Epot= -1.39088e+06 Fmax= 6.16702e+04, atom= 1704\n",
            "Step=   18, Dmax= 4.4e-02 nm, Epot= -1.39526e+06 Fmax= 2.37289e+04, atom= 1703\n",
            "Step=   19, Dmax= 5.3e-02 nm, Epot= -1.40305e+06 Fmax= 8.99231e+04, atom= 1703\n",
            "Step=   20, Dmax= 6.4e-02 nm, Epot= -1.40779e+06 Fmax= 2.54743e+04, atom= 1704\n",
            "Step=   21, Dmax= 7.7e-02 nm, Epot= -1.41450e+06 Fmax= 1.44284e+05, atom= 1703\n",
            "Step=   22, Dmax= 9.2e-02 nm, Epot= -1.42135e+06 Fmax= 1.99667e+04, atom= 1703\n",
            "Step=   23, Dmax= 1.1e-01 nm, Epot= -1.43317e+06 Fmax= 1.90641e+05, atom= 1703\n",
            "Step=   24, Dmax= 1.3e-01 nm, Epot= -1.43902e+06 Fmax= 2.39957e+04, atom= 1699\n",
            "Step=   25, Dmax= 1.6e-01 nm, Epot=  2.81871e+08 Fmax= 5.17072e+10, atom= 1699\rStep=   26, Dmax= 7.9e-02 nm, Epot= -1.44643e+06 Fmax= 1.63261e+05, atom= 1699\n",
            "Step=   27, Dmax= 9.5e-02 nm, Epot= -1.45174e+06 Fmax= 3.91496e+04, atom= 1704\n",
            "Step=   28, Dmax= 1.1e-01 nm, Epot= -1.45427e+06 Fmax= 1.29018e+05, atom= 1703\n",
            "Step=   29, Dmax= 1.4e-01 nm, Epot= -1.45633e+06 Fmax= 9.95049e+04, atom= 1699\n",
            "Step=   30, Dmax= 1.6e-01 nm, Epot= -1.33301e+06 Fmax= 1.19035e+07, atom= 1699\rStep=   31, Dmax= 8.2e-02 nm, Epot= -1.46009e+06 Fmax= 5.81496e+04, atom= 1704\n",
            "Step=   32, Dmax= 9.9e-02 nm, Epot= -1.46559e+06 Fmax= 6.38630e+04, atom= 1703\n",
            "Step=   33, Dmax= 1.2e-01 nm, Epot= -1.46977e+06 Fmax= 3.45355e+04, atom= 1703\n",
            "Step=   34, Dmax= 1.4e-01 nm, Epot= -1.44783e+06 Fmax= 4.23024e+05, atom= 1704\rStep=   35, Dmax= 7.1e-02 nm, Epot= -1.47389e+06 Fmax= 4.64549e+04, atom= 1703\n",
            "Step=   36, Dmax= 8.5e-02 nm, Epot= -1.47547e+06 Fmax= 9.54764e+04, atom= 1704\n",
            "Step=   37, Dmax= 1.0e-01 nm, Epot= -1.47685e+06 Fmax= 1.20812e+05, atom= 1703\n",
            "Step=   38, Dmax= 1.2e-01 nm, Epot= -1.47959e+06 Fmax= 3.07396e+04, atom= 1704\n",
            "Step=   39, Dmax= 1.5e-01 nm, Epot=  2.12922e+07 Fmax= 3.36819e+09, atom= 1699\rStep=   40, Dmax= 7.4e-02 nm, Epot= -1.48405e+06 Fmax= 1.19239e+05, atom= 1699\n",
            "Step=   41, Dmax= 8.9e-02 nm, Epot= -1.48811e+06 Fmax= 2.02526e+04, atom= 1699\n",
            "Step=   42, Dmax= 1.1e-01 nm, Epot= -1.47841e+06 Fmax= 2.54969e+05, atom= 1704\rStep=   43, Dmax= 5.3e-02 nm, Epot= -1.49059e+06 Fmax= 6.61840e+04, atom= 1703\n",
            "Step=   44, Dmax= 6.4e-02 nm, Epot= -1.49342e+06 Fmax= 2.52340e+04, atom= 1704\n",
            "Step=   45, Dmax= 7.7e-02 nm, Epot= -1.49728e+06 Fmax= 5.60429e+04, atom= 1703\n",
            "Step=   46, Dmax= 9.2e-02 nm, Epot= -1.49670e+06 Fmax= 7.49883e+04, atom= 1703\rStep=   47, Dmax= 4.6e-02 nm, Epot= -1.49952e+06 Fmax= 2.30856e+04, atom= 1703\n",
            "Step=   48, Dmax= 5.5e-02 nm, Epot= -1.50277e+06 Fmax= 3.71480e+04, atom= 1703\n",
            "Step=   49, Dmax= 6.6e-02 nm, Epot= -1.50412e+06 Fmax= 4.00252e+04, atom= 1704\n",
            "Step=   50, Dmax= 7.9e-02 nm, Epot= -1.50666e+06 Fmax= 4.55413e+04, atom= 1703\n",
            "Step=   51, Dmax= 9.5e-02 nm, Epot= -1.50602e+06 Fmax= 6.49033e+04, atom= 1699\rStep=   52, Dmax= 4.8e-02 nm, Epot= -1.50915e+06 Fmax= 1.68454e+04, atom= 1703\n",
            "Step=   53, Dmax= 5.7e-02 nm, Epot= -1.51331e+06 Fmax= 3.67958e+04, atom= 1703\n",
            "Step=   54, Dmax= 6.9e-02 nm, Epot= -1.51384e+06 Fmax= 4.83252e+04, atom= 1704\n",
            "Step=   55, Dmax= 8.2e-02 nm, Epot= -1.51602e+06 Fmax= 4.76231e+04, atom= 1703\n",
            "Step=   56, Dmax= 9.9e-02 nm, Epot= -1.51482e+06 Fmax= 6.81902e+04, atom= 1699\rStep=   57, Dmax= 4.9e-02 nm, Epot= -1.51872e+06 Fmax= 1.56482e+04, atom= 1703\n",
            "Step=   58, Dmax= 5.9e-02 nm, Epot= -1.52267e+06 Fmax= 3.91671e+04, atom= 1703\n",
            "Step=   59, Dmax= 7.1e-02 nm, Epot= -1.52270e+06 Fmax= 4.89543e+04, atom= 1704\n",
            "Step=   60, Dmax= 8.5e-02 nm, Epot= -1.52481e+06 Fmax= 4.37233e+04, atom= 1703\n",
            "Step=   61, Dmax= 1.0e-01 nm, Epot= -1.52108e+06 Fmax= 9.38004e+04, atom= 1699\rStep=   62, Dmax= 5.1e-02 nm, Epot= -1.52748e+06 Fmax= 1.91751e+04, atom= 1703\n",
            "Step=   63, Dmax= 6.1e-02 nm, Epot= -1.52966e+06 Fmax= 2.67817e+04, atom= 1703\n",
            "Step=   64, Dmax= 7.4e-02 nm, Epot= -1.52128e+06 Fmax= 1.26274e+05, atom= 1704\rStep=   65, Dmax= 3.7e-02 nm, Epot= -1.53164e+06 Fmax= 2.50820e+04, atom= 1704\n",
            "Step=   66, Dmax= 4.4e-02 nm, Epot= -1.53279e+06 Fmax= 2.57435e+04, atom= 1704\n",
            "Step=   67, Dmax= 5.3e-02 nm, Epot= -1.53039e+06 Fmax= 3.67648e+04, atom= 1133\rStep=   68, Dmax= 2.7e-02 nm, Epot= -1.53521e+06 Fmax= 1.49274e+04, atom= 1703\n",
            "Step=   69, Dmax= 3.2e-02 nm, Epot= -1.53625e+06 Fmax= 3.41009e+04, atom= 1703\n",
            "Step=   70, Dmax= 3.8e-02 nm, Epot= -1.53777e+06 Fmax= 2.54301e+04, atom= 1704\n",
            "Step=   71, Dmax= 4.6e-02 nm, Epot= -1.53859e+06 Fmax= 4.66891e+04, atom= 1703\n",
            "Step=   72, Dmax= 5.5e-02 nm, Epot= -1.53977e+06 Fmax= 2.83123e+04, atom= 1703\n",
            "Step=   73, Dmax= 6.6e-02 nm, Epot= -1.53930e+06 Fmax= 7.57904e+04, atom= 1704\rStep=   74, Dmax= 3.3e-02 nm, Epot= -1.54189e+06 Fmax= 1.07154e+04, atom= 1699\n",
            "Step=   75, Dmax= 4.0e-02 nm, Epot= -1.54351e+06 Fmax= 2.32946e+04, atom= 1699\n",
            "Step=   76, Dmax= 4.8e-02 nm, Epot= -1.54085e+06 Fmax= 6.39818e+04, atom= 1703\rStep=   77, Dmax= 2.4e-02 nm, Epot= -1.54563e+06 Fmax= 1.96231e+04, atom= 1703\n",
            "Step=   78, Dmax= 2.9e-02 nm, Epot= -1.54650e+06 Fmax= 2.33963e+04, atom= 1704\n",
            "Step=   79, Dmax= 3.4e-02 nm, Epot= -1.54743e+06 Fmax= 3.56221e+04, atom= 1703\n",
            "Step=   80, Dmax= 4.1e-02 nm, Epot= -1.54830e+06 Fmax= 2.61502e+04, atom= 1704\n",
            "Step=   81, Dmax= 4.9e-02 nm, Epot= -1.54869e+06 Fmax= 6.02920e+04, atom= 1703\n",
            "Step=   82, Dmax= 5.9e-02 nm, Epot= -1.55014e+06 Fmax= 2.51249e+04, atom= 1703\n",
            "Step=   83, Dmax= 7.1e-02 nm, Epot= -1.54909e+06 Fmax= 1.01438e+05, atom= 1703\rStep=   84, Dmax= 3.5e-02 nm, Epot= -1.55198e+06 Fmax= 1.27070e+04, atom= 1699\n",
            "Step=   85, Dmax= 4.3e-02 nm, Epot= -1.55320e+06 Fmax= 3.52847e+04, atom= 1703\n",
            "Step=   86, Dmax= 5.1e-02 nm, Epot= -1.55350e+06 Fmax= 6.25570e+04, atom= 1703\n",
            "Step=   87, Dmax= 6.1e-02 nm, Epot= -1.55503e+06 Fmax= 3.20151e+04, atom= 1704\n",
            "Step=   88, Dmax= 7.4e-02 nm, Epot= -1.55540e+06 Fmax= 6.49886e+04, atom= 1703\n",
            "Step=   89, Dmax= 8.8e-02 nm, Epot= -1.55536e+06 Fmax= 1.37732e+05, atom= 1703\rStep=   90, Dmax= 4.4e-02 nm, Epot= -1.55775e+06 Fmax= 1.65366e+04, atom= 1703\n",
            "Step=   91, Dmax= 5.3e-02 nm, Epot= -1.55930e+06 Fmax= 5.10016e+04, atom= 1703\n",
            "Step=   92, Dmax= 6.4e-02 nm, Epot= -1.55946e+06 Fmax= 3.87002e+04, atom= 1704\n",
            "Step=   93, Dmax= 7.6e-02 nm, Epot= -1.56029e+06 Fmax= 5.67795e+04, atom= 1703\n",
            "Step=   94, Dmax= 9.2e-02 nm, Epot= -1.55919e+06 Fmax= 9.46139e+04, atom= 1703\rStep=   95, Dmax= 4.6e-02 nm, Epot= -1.56218e+06 Fmax= 1.67931e+04, atom= 1703\n",
            "Step=   96, Dmax= 5.5e-02 nm, Epot= -1.56391e+06 Fmax= 4.56970e+04, atom= 1703\n",
            "Step=   97, Dmax= 6.6e-02 nm, Epot= -1.56370e+06 Fmax= 4.15263e+04, atom= 1704\rStep=   98, Dmax= 3.3e-02 nm, Epot= -1.56506e+06 Fmax= 1.75974e+04, atom= 1704\n",
            "Step=   99, Dmax= 4.0e-02 nm, Epot= -1.56569e+06 Fmax= 4.57279e+04, atom= 1704\n",
            "Step=  100, Dmax= 4.7e-02 nm, Epot= -1.56635e+06 Fmax= 2.73832e+04, atom= 1703\n",
            "Step=  101, Dmax= 5.7e-02 nm, Epot= -1.56634e+06 Fmax= 6.69637e+04, atom= 1703\rStep=  102, Dmax= 2.8e-02 nm, Epot= -1.56769e+06 Fmax= 7.91705e+03, atom= 1699\n",
            "Step=  103, Dmax= 3.4e-02 nm, Epot= -1.56940e+06 Fmax= 2.94841e+04, atom= 1703\n",
            "Step=  104, Dmax= 4.1e-02 nm, Epot= -1.56960e+06 Fmax= 5.53540e+04, atom= 1703\n",
            "Step=  105, Dmax= 4.9e-02 nm, Epot= -1.57066e+06 Fmax= 2.85200e+04, atom= 1704\n",
            "Step=  106, Dmax= 5.9e-02 nm, Epot= -1.57064e+06 Fmax= 6.60433e+04, atom= 1704\rStep=  107, Dmax= 3.0e-02 nm, Epot= -1.57189e+06 Fmax= 6.29720e+03, atom= 1699\n",
            "Step=  108, Dmax= 3.5e-02 nm, Epot= -1.57340e+06 Fmax= 4.06682e+04, atom= 1704\n",
            "Step=  109, Dmax= 4.3e-02 nm, Epot= -1.57441e+06 Fmax= 4.88688e+04, atom= 1703\n",
            "Step=  110, Dmax= 5.1e-02 nm, Epot= -1.57491e+06 Fmax= 2.97203e+04, atom= 1704\n",
            "Step=  111, Dmax= 6.1e-02 nm, Epot= -1.57439e+06 Fmax= 7.71062e+04, atom= 1703\rStep=  112, Dmax= 3.1e-02 nm, Epot= -1.57635e+06 Fmax= 8.62374e+03, atom= 1699\n",
            "Step=  113, Dmax= 3.7e-02 nm, Epot= -1.57764e+06 Fmax= 3.15874e+04, atom= 1703\n",
            "Step=  114, Dmax= 4.4e-02 nm, Epot= -1.57751e+06 Fmax= 6.38521e+04, atom= 1703\rStep=  115, Dmax= 2.2e-02 nm, Epot= -1.57882e+06 Fmax= 1.03843e+04, atom= 1703\n",
            "Step=  116, Dmax= 2.6e-02 nm, Epot= -1.57956e+06 Fmax= 2.40946e+04, atom= 1704\n",
            "Step=  117, Dmax= 3.2e-02 nm, Epot= -1.58027e+06 Fmax= 2.74802e+04, atom= 1704\n",
            "Step=  118, Dmax= 3.8e-02 nm, Epot= -1.58046e+06 Fmax= 2.82924e+04, atom= 1703\n",
            "Step=  119, Dmax= 4.6e-02 nm, Epot= -1.58086e+06 Fmax= 4.77529e+04, atom= 1703\n",
            "Step=  120, Dmax= 5.5e-02 nm, Epot= -1.58136e+06 Fmax= 2.81737e+04, atom= 1703\n",
            "Step=  121, Dmax= 6.6e-02 nm, Epot= -1.58061e+06 Fmax= 7.95374e+04, atom= 1704\rStep=  122, Dmax= 3.3e-02 nm, Epot= -1.58285e+06 Fmax= 1.15920e+04, atom= 1699\n",
            "Step=  123, Dmax= 3.9e-02 nm, Epot= -1.58405e+06 Fmax= 2.36210e+04, atom= 1699\n",
            "Step=  124, Dmax= 4.7e-02 nm, Epot= -1.58309e+06 Fmax= 7.10233e+04, atom= 1703\rStep=  125, Dmax= 2.4e-02 nm, Epot= -1.58479e+06 Fmax= 2.01141e+04, atom= 1703\n",
            "Step=  126, Dmax= 2.8e-02 nm, Epot= -1.58512e+06 Fmax= 2.34574e+04, atom= 1704\n",
            "Step=  127, Dmax= 3.4e-02 nm, Epot= -1.58555e+06 Fmax= 3.58709e+04, atom= 1703\n",
            "Step=  128, Dmax= 4.1e-02 nm, Epot= -1.58590e+06 Fmax= 2.64264e+04, atom= 1703\n",
            "Step=  129, Dmax= 4.9e-02 nm, Epot= -1.58579e+06 Fmax= 5.99773e+04, atom= 1703\rStep=  130, Dmax= 2.5e-02 nm, Epot= -1.58700e+06 Fmax= 6.47927e+03, atom= 1699\n",
            "Step=  131, Dmax= 2.9e-02 nm, Epot= -1.58833e+06 Fmax= 2.54681e+04, atom= 1703\n",
            "Step=  132, Dmax= 3.5e-02 nm, Epot= -1.58836e+06 Fmax= 5.06678e+04, atom= 1703\n",
            "Step=  133, Dmax= 4.2e-02 nm, Epot= -1.58924e+06 Fmax= 2.59528e+04, atom= 1704\n",
            "Step=  134, Dmax= 5.1e-02 nm, Epot= -1.58883e+06 Fmax= 6.56704e+04, atom= 1704\rStep=  135, Dmax= 2.5e-02 nm, Epot= -1.59012e+06 Fmax= 6.84942e+03, atom= 1704\n",
            "Step=  136, Dmax= 3.1e-02 nm, Epot= -1.59035e+06 Fmax= 4.00270e+04, atom= 1703\n",
            "Step=  137, Dmax= 3.7e-02 nm, Epot= -1.59198e+06 Fmax= 2.08291e+04, atom= 1703\n",
            "Step=  138, Dmax= 4.4e-02 nm, Epot= -1.59144e+06 Fmax= 3.77098e+04, atom= 1703\rStep=  139, Dmax= 2.2e-02 nm, Epot= -1.59245e+06 Fmax= 1.57716e+04, atom= 1704\n",
            "Step=  140, Dmax= 2.6e-02 nm, Epot= -1.59280e+06 Fmax= 3.11720e+04, atom= 1703\n",
            "Step=  141, Dmax= 3.2e-02 nm, Epot= -1.59324e+06 Fmax= 2.15694e+04, atom= 1704\n",
            "Step=  142, Dmax= 3.8e-02 nm, Epot= -1.59323e+06 Fmax= 4.88815e+04, atom= 1703\rStep=  143, Dmax= 1.9e-02 nm, Epot= -1.59394e+06 Fmax= 4.61573e+03, atom= 1699\n",
            "Step=  144, Dmax= 2.3e-02 nm, Epot= -1.59478e+06 Fmax= 3.37945e+04, atom= 1703\n",
            "Step=  145, Dmax= 2.7e-02 nm, Epot= -1.59596e+06 Fmax= 1.34129e+04, atom= 1703\n",
            "Step=  146, Dmax= 3.3e-02 nm, Epot= -1.59591e+06 Fmax= 3.23728e+04, atom= 1703\rStep=  147, Dmax= 1.6e-02 nm, Epot= -1.59634e+06 Fmax= 1.43778e+04, atom= 1704\n",
            "Step=  148, Dmax= 2.0e-02 nm, Epot= -1.59673e+06 Fmax= 2.10609e+04, atom= 1703\n",
            "Step=  149, Dmax= 2.4e-02 nm, Epot= -1.59707e+06 Fmax= 1.89883e+04, atom= 1704\n",
            "Step=  150, Dmax= 2.8e-02 nm, Epot= -1.59734e+06 Fmax= 3.28727e+04, atom= 1703\n",
            "Step=  151, Dmax= 3.4e-02 nm, Epot= -1.59770e+06 Fmax= 2.33945e+04, atom= 1704\n",
            "Step=  152, Dmax= 4.1e-02 nm, Epot= -1.59756e+06 Fmax= 5.28136e+04, atom= 1703\rStep=  153, Dmax= 2.0e-02 nm, Epot= -1.59847e+06 Fmax= 5.09208e+03, atom= 1699\n",
            "Step=  154, Dmax= 2.5e-02 nm, Epot= -1.59921e+06 Fmax= 3.31574e+04, atom= 1703\n",
            "Step=  155, Dmax= 2.9e-02 nm, Epot= -1.60019e+06 Fmax= 2.07409e+04, atom= 1703\n",
            "Step=  156, Dmax= 3.5e-02 nm, Epot= -1.60004e+06 Fmax= 3.03155e+04, atom= 1703\rStep=  157, Dmax= 1.8e-02 nm, Epot= -1.60060e+06 Fmax= 1.18793e+04, atom= 1704\n",
            "Step=  158, Dmax= 2.1e-02 nm, Epot= -1.60090e+06 Fmax= 2.75920e+04, atom= 1704\n",
            "Step=  159, Dmax= 2.5e-02 nm, Epot= -1.60132e+06 Fmax= 1.76598e+04, atom= 1703\n",
            "Step=  160, Dmax= 3.1e-02 nm, Epot= -1.60133e+06 Fmax= 4.17398e+04, atom= 1703\n",
            "Step=  161, Dmax= 3.7e-02 nm, Epot= -1.60192e+06 Fmax= 2.23991e+04, atom= 1704\n",
            "Step=  162, Dmax= 4.4e-02 nm, Epot= -1.60132e+06 Fmax= 6.44895e+04, atom= 1704\rStep=  163, Dmax= 2.2e-02 nm, Epot= -1.60261e+06 Fmax= 8.01357e+03, atom= 1704\n",
            "Step=  164, Dmax= 2.6e-02 nm, Epot= -1.60270e+06 Fmax= 3.36046e+04, atom= 1703\n",
            "Step=  165, Dmax= 3.2e-02 nm, Epot= -1.60380e+06 Fmax= 1.72772e+04, atom= 1703\n",
            "Step=  166, Dmax= 3.8e-02 nm, Epot= -1.60335e+06 Fmax= 3.57921e+04, atom= 1703\rStep=  167, Dmax= 1.9e-02 nm, Epot= -1.60416e+06 Fmax= 1.47786e+04, atom= 1704\n",
            "Step=  168, Dmax= 2.3e-02 nm, Epot= -1.60445e+06 Fmax= 2.59952e+04, atom= 1703\n",
            "Step=  169, Dmax= 2.7e-02 nm, Epot= -1.60477e+06 Fmax= 2.02241e+04, atom= 1704\n",
            "Step=  170, Dmax= 3.3e-02 nm, Epot= -1.60483e+06 Fmax= 4.05357e+04, atom= 1703\n",
            "Step=  171, Dmax= 3.9e-02 nm, Epot= -1.60527e+06 Fmax= 2.44906e+04, atom= 1703\n",
            "Step=  172, Dmax= 4.7e-02 nm, Epot= -1.60468e+06 Fmax= 6.47421e+04, atom= 1703\rStep=  173, Dmax= 2.4e-02 nm, Epot= -1.60609e+06 Fmax= 6.66385e+03, atom= 1699\n",
            "Step=  174, Dmax= 2.8e-02 nm, Epot= -1.60617e+06 Fmax= 3.80645e+04, atom= 1703\n",
            "Step=  175, Dmax= 3.4e-02 nm, Epot= -1.60741e+06 Fmax= 2.12460e+04, atom= 1703\n",
            "Step=  176, Dmax= 4.1e-02 nm, Epot= -1.60692e+06 Fmax= 3.44639e+04, atom= 1703\rStep=  177, Dmax= 2.0e-02 nm, Epot= -1.60778e+06 Fmax= 1.45936e+04, atom= 1704\n",
            "Step=  178, Dmax= 2.4e-02 nm, Epot= -1.60798e+06 Fmax= 2.96381e+04, atom= 1704\n",
            "Step=  179, Dmax= 2.9e-02 nm, Epot= -1.60832e+06 Fmax= 2.05613e+04, atom= 1703\n",
            "Step=  180, Dmax= 3.5e-02 nm, Epot= -1.60820e+06 Fmax= 4.61056e+04, atom= 1703\rStep=  181, Dmax= 1.8e-02 nm, Epot= -1.60889e+06 Fmax= 4.72804e+03, atom= 1703\n",
            "Step=  182, Dmax= 2.1e-02 nm, Epot= -1.60934e+06 Fmax= 3.09963e+04, atom= 1703\n",
            "Step=  183, Dmax= 2.5e-02 nm, Epot= -1.61030e+06 Fmax= 1.18069e+04, atom= 1703\n",
            "Step=  184, Dmax= 3.0e-02 nm, Epot= -1.61013e+06 Fmax= 3.18879e+04, atom= 1703\rStep=  185, Dmax= 1.5e-02 nm, Epot= -1.61059e+06 Fmax= 1.40073e+04, atom= 1704\n",
            "Step=  186, Dmax= 1.8e-02 nm, Epot= -1.61089e+06 Fmax= 1.89371e+04, atom= 1703\n",
            "Step=  187, Dmax= 2.2e-02 nm, Epot= -1.61113e+06 Fmax= 1.83781e+04, atom= 1704\n",
            "Step=  188, Dmax= 2.6e-02 nm, Epot= -1.61133e+06 Fmax= 2.97287e+04, atom= 1703\n",
            "Step=  189, Dmax= 3.2e-02 nm, Epot= -1.61158e+06 Fmax= 2.28680e+04, atom= 1703\n",
            "Step=  190, Dmax= 3.8e-02 nm, Epot= -1.61144e+06 Fmax= 4.76538e+04, atom= 1703\rStep=  191, Dmax= 1.9e-02 nm, Epot= -1.61224e+06 Fmax= 4.42185e+03, atom= 1699\n",
            "Step=  192, Dmax= 2.3e-02 nm, Epot= -1.61284e+06 Fmax= 3.06409e+04, atom= 1703\n",
            "Step=  193, Dmax= 2.7e-02 nm, Epot= -1.61362e+06 Fmax= 2.07626e+04, atom= 1703\n",
            "Step=  194, Dmax= 3.3e-02 nm, Epot= -1.61346e+06 Fmax= 2.86626e+04, atom= 1704\rStep=  195, Dmax= 1.6e-02 nm, Epot= -1.61396e+06 Fmax= 1.03803e+04, atom= 1704\n",
            "Step=  196, Dmax= 2.0e-02 nm, Epot= -1.61417e+06 Fmax= 2.69114e+04, atom= 1704\n",
            "Step=  197, Dmax= 2.4e-02 nm, Epot= -1.61453e+06 Fmax= 1.61038e+04, atom= 1703\n",
            "Step=  198, Dmax= 2.8e-02 nm, Epot= -1.61446e+06 Fmax= 3.98790e+04, atom= 1703\rStep=  199, Dmax= 1.4e-02 nm, Epot= -1.61491e+06 Fmax= 6.48216e+03, atom= 1703\n",
            "Step=  200, Dmax= 1.7e-02 nm, Epot= -1.61523e+06 Fmax= 2.13522e+04, atom= 1703\n",
            "Step=  201, Dmax= 2.0e-02 nm, Epot= -1.61572e+06 Fmax= 1.33284e+04, atom= 1703\n",
            "Step=  202, Dmax= 2.4e-02 nm, Epot= -1.61575e+06 Fmax= 2.49978e+04, atom= 1703\n",
            "Step=  203, Dmax= 2.9e-02 nm, Epot= -1.61621e+06 Fmax= 2.51666e+04, atom= 1703\n",
            "Step=  204, Dmax= 3.5e-02 nm, Epot= -1.61609e+06 Fmax= 2.85556e+04, atom= 1703\rStep=  205, Dmax= 1.8e-02 nm, Epot= -1.61668e+06 Fmax= 8.29174e+03, atom= 1704\n",
            "Step=  206, Dmax= 2.1e-02 nm, Epot= -1.61686e+06 Fmax= 3.30083e+04, atom= 1704\n",
            "Step=  207, Dmax= 2.5e-02 nm, Epot= -1.61734e+06 Fmax= 1.54277e+04, atom= 1704\n",
            "Step=  208, Dmax= 3.0e-02 nm, Epot= -1.61702e+06 Fmax= 4.78527e+04, atom= 1703\rStep=  209, Dmax= 1.5e-02 nm, Epot= -1.61769e+06 Fmax= 9.73669e+03, atom= 1703\n",
            "Step=  210, Dmax= 1.8e-02 nm, Epot= -1.61787e+06 Fmax= 2.01094e+04, atom= 1703\n",
            "Step=  211, Dmax= 2.2e-02 nm, Epot= -1.61827e+06 Fmax= 1.77651e+04, atom= 1703\n",
            "Step=  212, Dmax= 2.6e-02 nm, Epot= -1.61828e+06 Fmax= 2.41986e+04, atom= 1703\n",
            "Step=  213, Dmax= 3.2e-02 nm, Epot= -1.61858e+06 Fmax= 3.08920e+04, atom= 1703\n",
            "Step=  214, Dmax= 3.8e-02 nm, Epot= -1.61859e+06 Fmax= 2.77720e+04, atom= 1703\n",
            "Step=  215, Dmax= 4.5e-02 nm, Epot= -1.61845e+06 Fmax= 5.15063e+04, atom= 1703\rStep=  216, Dmax= 2.3e-02 nm, Epot= -1.61950e+06 Fmax= 5.38350e+03, atom= 1699\n",
            "Step=  217, Dmax= 2.7e-02 nm, Epot= -1.62042e+06 Fmax= 1.85042e+04, atom= 1699\n",
            "Step=  218, Dmax= 3.3e-02 nm, Epot= -1.62029e+06 Fmax= 4.00822e+04, atom= 1703\rStep=  219, Dmax= 1.6e-02 nm, Epot= -1.62081e+06 Fmax= 1.30645e+04, atom= 1703\n",
            "Step=  220, Dmax= 2.0e-02 nm, Epot= -1.62098e+06 Fmax= 1.84606e+04, atom= 1704\n",
            "Step=  221, Dmax= 2.4e-02 nm, Epot= -1.62119e+06 Fmax= 2.54503e+04, atom= 1703\n",
            "Step=  222, Dmax= 2.8e-02 nm, Epot= -1.62133e+06 Fmax= 2.23517e+04, atom= 1704\n",
            "Step=  223, Dmax= 3.4e-02 nm, Epot= -1.62129e+06 Fmax= 4.09077e+04, atom= 1703\rStep=  224, Dmax= 1.7e-02 nm, Epot= -1.62190e+06 Fmax= 3.31083e+03, atom= 1699\n",
            "Step=  225, Dmax= 2.0e-02 nm, Epot= -1.62265e+06 Fmax= 2.70003e+04, atom= 1703\n",
            "Step=  226, Dmax= 2.4e-02 nm, Epot= -1.62322e+06 Fmax= 2.13200e+04, atom= 1703\n",
            "Step=  227, Dmax= 2.9e-02 nm, Epot= -1.62315e+06 Fmax= 2.59673e+04, atom= 1704\rStep=  228, Dmax= 1.5e-02 nm, Epot= -1.62355e+06 Fmax= 7.89354e+03, atom= 1704\n",
            "Step=  229, Dmax= 1.8e-02 nm, Epot= -1.62373e+06 Fmax= 2.62018e+04, atom= 1704\n",
            "Step=  230, Dmax= 2.1e-02 nm, Epot= -1.62408e+06 Fmax= 1.37000e+04, atom= 1703\n",
            "Step=  231, Dmax= 2.5e-02 nm, Epot= -1.62397e+06 Fmax= 3.73542e+04, atom= 1703\rStep=  232, Dmax= 1.3e-02 nm, Epot= -1.62437e+06 Fmax= 7.52074e+03, atom= 1703\n",
            "Step=  233, Dmax= 1.5e-02 nm, Epot= -1.62458e+06 Fmax= 1.80223e+04, atom= 1703\n",
            "Step=  234, Dmax= 1.8e-02 nm, Epot= -1.62492e+06 Fmax= 1.39168e+04, atom= 1703\n",
            "Step=  235, Dmax= 2.2e-02 nm, Epot= -1.62497e+06 Fmax= 2.19106e+04, atom= 1703\n",
            "Step=  236, Dmax= 2.6e-02 nm, Epot= -1.62527e+06 Fmax= 2.45224e+04, atom= 1703\n",
            "Step=  237, Dmax= 3.1e-02 nm, Epot= -1.62524e+06 Fmax= 2.59749e+04, atom= 1703\rStep=  238, Dmax= 1.6e-02 nm, Epot= -1.62569e+06 Fmax= 6.32887e+03, atom= 1704\n",
            "Step=  239, Dmax= 1.9e-02 nm, Epot= -1.62589e+06 Fmax= 3.14417e+04, atom= 1704\n",
            "Step=  240, Dmax= 2.3e-02 nm, Epot= -1.62634e+06 Fmax= 1.32178e+04, atom= 1704\n",
            "Step=  241, Dmax= 2.7e-02 nm, Epot= -1.62603e+06 Fmax= 4.45963e+04, atom= 1703\rStep=  242, Dmax= 1.4e-02 nm, Epot= -1.62660e+06 Fmax= 1.05234e+04, atom= 1703\n",
            "Step=  243, Dmax= 1.6e-02 nm, Epot= -1.62676e+06 Fmax= 1.71717e+04, atom= 1704\n",
            "Step=  244, Dmax= 2.0e-02 nm, Epot= -1.62703e+06 Fmax= 1.78747e+04, atom= 1703\n",
            "Step=  245, Dmax= 2.4e-02 nm, Epot= -1.62709e+06 Fmax= 2.13440e+04, atom= 1703\n",
            "Step=  246, Dmax= 2.8e-02 nm, Epot= -1.62726e+06 Fmax= 2.97073e+04, atom= 1703\n",
            "Step=  247, Dmax= 3.4e-02 nm, Epot= -1.62733e+06 Fmax= 2.55151e+04, atom= 1703\n",
            "Step=  248, Dmax= 4.1e-02 nm, Epot= -1.62714e+06 Fmax= 4.83456e+04, atom= 1703\rStep=  249, Dmax= 2.0e-02 nm, Epot= -1.62806e+06 Fmax= 4.61713e+03, atom= 1699\n",
            "Step=  250, Dmax= 2.4e-02 nm, Epot= -1.62866e+06 Fmax= 2.27062e+04, atom= 1703\n",
            "Step=  251, Dmax= 2.9e-02 nm, Epot= -1.62861e+06 Fmax= 4.13414e+04, atom= 1703\rStep=  252, Dmax= 1.5e-02 nm, Epot= -1.62918e+06 Fmax= 6.83176e+03, atom= 1703\n",
            "Step=  253, Dmax= 1.8e-02 nm, Epot= -1.62946e+06 Fmax= 1.84818e+04, atom= 1704\n",
            "Step=  254, Dmax= 2.1e-02 nm, Epot= -1.62975e+06 Fmax= 1.74176e+04, atom= 1704\n",
            "Step=  255, Dmax= 2.5e-02 nm, Epot= -1.62972e+06 Fmax= 2.34404e+04, atom= 1703\rStep=  256, Dmax= 1.3e-02 nm, Epot= -1.63002e+06 Fmax= 6.81127e+03, atom= 1703\n",
            "Step=  257, Dmax= 1.5e-02 nm, Epot= -1.63023e+06 Fmax= 2.20057e+04, atom= 1703\n",
            "Step=  258, Dmax= 1.8e-02 nm, Epot= -1.63051e+06 Fmax= 1.24867e+04, atom= 1704\n",
            "Step=  259, Dmax= 2.2e-02 nm, Epot= -1.63049e+06 Fmax= 3.07564e+04, atom= 1704\rStep=  260, Dmax= 1.1e-02 nm, Epot= -1.63075e+06 Fmax= 6.09771e+03, atom= 1703\n",
            "Step=  261, Dmax= 1.3e-02 nm, Epot= -1.63097e+06 Fmax= 1.62105e+04, atom= 1704\n",
            "Step=  262, Dmax= 1.6e-02 nm, Epot= -1.63126e+06 Fmax= 1.16137e+04, atom= 1703\n",
            "Step=  263, Dmax= 1.9e-02 nm, Epot= -1.63132e+06 Fmax= 1.98378e+04, atom= 1703\n",
            "Step=  264, Dmax= 2.3e-02 nm, Epot= -1.63160e+06 Fmax= 2.06147e+04, atom= 1703\n",
            "Step=  265, Dmax= 2.7e-02 nm, Epot= -1.63158e+06 Fmax= 2.39871e+04, atom= 1703\rStep=  266, Dmax= 1.4e-02 nm, Epot= -1.63193e+06 Fmax= 5.91041e+03, atom= 1704\n",
            "Step=  267, Dmax= 1.6e-02 nm, Epot= -1.63212e+06 Fmax= 2.63992e+04, atom= 1704\n",
            "Step=  268, Dmax= 2.0e-02 nm, Epot= -1.63248e+06 Fmax= 1.17678e+04, atom= 1704\n",
            "Step=  269, Dmax= 2.3e-02 nm, Epot= -1.63231e+06 Fmax= 3.69702e+04, atom= 1704\rStep=  270, Dmax= 1.2e-02 nm, Epot= -1.63270e+06 Fmax= 8.82585e+03, atom= 1703\n",
            "Step=  271, Dmax= 1.4e-02 nm, Epot= -1.63285e+06 Fmax= 1.54575e+04, atom= 1704\n",
            "Step=  272, Dmax= 1.7e-02 nm, Epot= -1.63310e+06 Fmax= 1.49590e+04, atom= 1703\n",
            "Step=  273, Dmax= 2.0e-02 nm, Epot= -1.63316e+06 Fmax= 1.94340e+04, atom= 1703\n",
            "Step=  274, Dmax= 2.4e-02 nm, Epot= -1.63334e+06 Fmax= 2.48725e+04, atom= 1703\n",
            "Step=  275, Dmax= 2.9e-02 nm, Epot= -1.63338e+06 Fmax= 2.37778e+04, atom= 1703\n",
            "Step=  276, Dmax= 3.5e-02 nm, Epot= -1.63333e+06 Fmax= 4.04168e+04, atom= 1703\rStep=  277, Dmax= 1.8e-02 nm, Epot= -1.63398e+06 Fmax= 3.38484e+03, atom= 1699\n",
            "Step=  278, Dmax= 2.1e-02 nm, Epot= -1.63473e+06 Fmax= 1.86558e+04, atom= 1703\n",
            "Step=  279, Dmax= 2.5e-02 nm, Epot= -1.63466e+06 Fmax= 3.76282e+04, atom= 1703\rStep=  280, Dmax= 1.3e-02 nm, Epot= -1.63512e+06 Fmax= 7.72870e+03, atom= 1703\n",
            "Step=  281, Dmax= 1.5e-02 nm, Epot= -1.63532e+06 Fmax= 1.59942e+04, atom= 1704\n",
            "Step=  282, Dmax= 1.8e-02 nm, Epot= -1.63553e+06 Fmax= 1.66778e+04, atom= 1704\n",
            "Step=  283, Dmax= 2.2e-02 nm, Epot= -1.63557e+06 Fmax= 2.02549e+04, atom= 1704\n",
            "Step=  284, Dmax= 2.6e-02 nm, Epot= -1.63571e+06 Fmax= 2.79133e+04, atom= 1703\n",
            "Step=  285, Dmax= 3.1e-02 nm, Epot= -1.63576e+06 Fmax= 2.45181e+04, atom= 1703\n",
            "Step=  286, Dmax= 3.8e-02 nm, Epot= -1.63558e+06 Fmax= 4.50565e+04, atom= 1703\rStep=  287, Dmax= 1.9e-02 nm, Epot= -1.63639e+06 Fmax= 4.03554e+03, atom= 1699\n",
            "Step=  288, Dmax= 2.3e-02 nm, Epot= -1.63685e+06 Fmax= 2.38338e+04, atom= 1703\n",
            "Step=  289, Dmax= 2.7e-02 nm, Epot= -1.63699e+06 Fmax= 3.43107e+04, atom= 1703\n",
            "Step=  290, Dmax= 3.3e-02 nm, Epot= -1.63720e+06 Fmax= 2.43434e+04, atom= 1704\n",
            "Step=  291, Dmax= 3.9e-02 nm, Epot= -1.63678e+06 Fmax= 5.11273e+04, atom= 1704\rStep=  292, Dmax= 2.0e-02 nm, Epot= -1.63774e+06 Fmax= 4.96267e+03, atom= 1703\n",
            "Step=  293, Dmax= 2.3e-02 nm, Epot= -1.63752e+06 Fmax= 3.44510e+04, atom= 1703\rStep=  294, Dmax= 1.2e-02 nm, Epot= -1.63796e+06 Fmax= 1.61707e+04, atom= 1703\n",
            "Step=  295, Dmax= 1.4e-02 nm, Epot= -1.63824e+06 Fmax= 8.40231e+03, atom= 1703\n",
            "Step=  296, Dmax= 1.7e-02 nm, Epot= -1.63832e+06 Fmax= 1.92565e+04, atom= 1703\n",
            "Step=  297, Dmax= 2.0e-02 nm, Epot= -1.63861e+06 Fmax= 1.64610e+04, atom= 1703\n",
            "Step=  298, Dmax= 2.4e-02 nm, Epot= -1.63855e+06 Fmax= 2.32375e+04, atom= 1703\rStep=  299, Dmax= 1.2e-02 nm, Epot= -1.63884e+06 Fmax= 6.71107e+03, atom= 1704\n",
            "Step=  300, Dmax= 1.5e-02 nm, Epot= -1.63899e+06 Fmax= 2.14660e+04, atom= 1704\n",
            "Step=  301, Dmax= 1.7e-02 nm, Epot= -1.63924e+06 Fmax= 1.17188e+04, atom= 1704\n",
            "Step=  302, Dmax= 2.1e-02 nm, Epot= -1.63918e+06 Fmax= 3.01741e+04, atom= 1704\rStep=  303, Dmax= 1.0e-02 nm, Epot= -1.63945e+06 Fmax= 6.29711e+03, atom= 1703\n",
            "Step=  304, Dmax= 1.3e-02 nm, Epot= -1.63961e+06 Fmax= 1.53493e+04, atom= 1704\n",
            "Step=  305, Dmax= 1.5e-02 nm, Epot= -1.63985e+06 Fmax= 1.15130e+04, atom= 1703\n",
            "Step=  306, Dmax= 1.8e-02 nm, Epot= -1.63989e+06 Fmax= 1.89934e+04, atom= 1703\n",
            "Step=  307, Dmax= 2.2e-02 nm, Epot= -1.64012e+06 Fmax= 2.00937e+04, atom= 1703\n",
            "Step=  308, Dmax= 2.6e-02 nm, Epot= -1.64009e+06 Fmax= 2.31930e+04, atom= 1703\rStep=  309, Dmax= 1.3e-02 nm, Epot= -1.64041e+06 Fmax= 5.49155e+03, atom= 1704\n",
            "Step=  310, Dmax= 1.6e-02 nm, Epot= -1.64057e+06 Fmax= 2.56081e+04, atom= 1704\n",
            "Step=  311, Dmax= 1.9e-02 nm, Epot= -1.64089e+06 Fmax= 1.12024e+04, atom= 1704\n",
            "Step=  312, Dmax= 2.3e-02 nm, Epot= -1.64070e+06 Fmax= 3.56828e+04, atom= 1704\rStep=  313, Dmax= 1.1e-02 nm, Epot= -1.64107e+06 Fmax= 8.76139e+03, atom= 1703\n",
            "Step=  314, Dmax= 1.4e-02 nm, Epot= -1.64119e+06 Fmax= 1.47566e+04, atom= 1704\n",
            "Step=  315, Dmax= 1.6e-02 nm, Epot= -1.64139e+06 Fmax= 1.46428e+04, atom= 1703\n",
            "Step=  316, Dmax= 1.9e-02 nm, Epot= -1.64144e+06 Fmax= 1.86933e+04, atom= 1703\n",
            "Step=  317, Dmax= 2.3e-02 nm, Epot= -1.64159e+06 Fmax= 2.41350e+04, atom= 1703\n",
            "Step=  318, Dmax= 2.8e-02 nm, Epot= -1.64161e+06 Fmax= 2.30779e+04, atom= 1703\n",
            "Step=  319, Dmax= 3.4e-02 nm, Epot= -1.64153e+06 Fmax= 3.90035e+04, atom= 1703\rStep=  320, Dmax= 1.7e-02 nm, Epot= -1.64215e+06 Fmax= 3.19335e+03, atom= 1699\n",
            "Step=  321, Dmax= 2.0e-02 nm, Epot= -1.64274e+06 Fmax= 1.97118e+04, atom= 1703\n",
            "Step=  322, Dmax= 2.4e-02 nm, Epot= -1.64275e+06 Fmax= 3.35045e+04, atom= 1703\n",
            "Step=  323, Dmax= 2.9e-02 nm, Epot= -1.64305e+06 Fmax= 2.11199e+04, atom= 1704\n",
            "Step=  324, Dmax= 3.5e-02 nm, Epot= -1.64262e+06 Fmax= 4.79490e+04, atom= 1704\rStep=  325, Dmax= 1.7e-02 nm, Epot= -1.64345e+06 Fmax= 6.48700e+03, atom= 1703\n",
            "Step=  326, Dmax= 2.1e-02 nm, Epot= -1.64332e+06 Fmax= 2.74116e+04, atom= 1703\rStep=  327, Dmax= 1.0e-02 nm, Epot= -1.64361e+06 Fmax= 1.22972e+04, atom= 1703\n",
            "Step=  328, Dmax= 1.3e-02 nm, Epot= -1.64379e+06 Fmax= 1.01003e+04, atom= 1703\n",
            "Step=  329, Dmax= 1.5e-02 nm, Epot= -1.64388e+06 Fmax= 1.58592e+04, atom= 1704\n",
            "Step=  330, Dmax= 1.8e-02 nm, Epot= -1.64407e+06 Fmax= 1.69947e+04, atom= 1703\n",
            "Step=  331, Dmax= 2.2e-02 nm, Epot= -1.64409e+06 Fmax= 1.99497e+04, atom= 1703\n",
            "Step=  332, Dmax= 2.6e-02 nm, Epot= -1.64418e+06 Fmax= 2.78866e+04, atom= 1703\n",
            "Step=  333, Dmax= 3.1e-02 nm, Epot= -1.64421e+06 Fmax= 2.43103e+04, atom= 1703\n",
            "Step=  334, Dmax= 3.8e-02 nm, Epot= -1.64399e+06 Fmax= 4.49687e+04, atom= 1703\rStep=  335, Dmax= 1.9e-02 nm, Epot= -1.64481e+06 Fmax= 4.06394e+03, atom= 1699\n",
            "Step=  336, Dmax= 2.3e-02 nm, Epot= -1.64512e+06 Fmax= 2.41492e+04, atom= 1703\n",
            "Step=  337, Dmax= 2.7e-02 nm, Epot= -1.64525e+06 Fmax= 3.33690e+04, atom= 1703\n",
            "Step=  338, Dmax= 3.2e-02 nm, Epot= -1.64540e+06 Fmax= 2.45358e+04, atom= 1704\n",
            "Step=  339, Dmax= 3.9e-02 nm, Epot= -1.64498e+06 Fmax= 5.03303e+04, atom= 1704\rStep=  340, Dmax= 1.9e-02 nm, Epot= -1.64595e+06 Fmax= 4.54033e+03, atom= 1703\n",
            "Step=  341, Dmax= 2.3e-02 nm, Epot= -1.64560e+06 Fmax= 3.55428e+04, atom= 1703\rStep=  342, Dmax= 1.2e-02 nm, Epot= -1.64612e+06 Fmax= 1.66966e+04, atom= 1703\n",
            "Step=  343, Dmax= 1.4e-02 nm, Epot= -1.64639e+06 Fmax= 7.84056e+03, atom= 1703\n",
            "Step=  344, Dmax= 1.7e-02 nm, Epot= -1.64642e+06 Fmax= 1.94982e+04, atom= 1703\n",
            "Step=  345, Dmax= 2.0e-02 nm, Epot= -1.64670e+06 Fmax= 1.59811e+04, atom= 1703\n",
            "Step=  346, Dmax= 2.4e-02 nm, Epot= -1.64659e+06 Fmax= 2.34652e+04, atom= 1703\rStep=  347, Dmax= 1.2e-02 nm, Epot= -1.64692e+06 Fmax= 7.00753e+03, atom= 1704\n",
            "Step=  348, Dmax= 1.5e-02 nm, Epot= -1.64700e+06 Fmax= 2.09895e+04, atom= 1704\n",
            "Step=  349, Dmax= 1.7e-02 nm, Epot= -1.64723e+06 Fmax= 1.19323e+04, atom= 1704\n",
            "Step=  350, Dmax= 2.1e-02 nm, Epot= -1.64714e+06 Fmax= 2.95965e+04, atom= 1704\rStep=  351, Dmax= 1.0e-02 nm, Epot= -1.64742e+06 Fmax= 5.93547e+03, atom= 1703\n",
            "Step=  352, Dmax= 1.3e-02 nm, Epot= -1.64754e+06 Fmax= 1.56111e+04, atom= 1704\n",
            "Step=  353, Dmax= 1.5e-02 nm, Epot= -1.64776e+06 Fmax= 1.11011e+04, atom= 1703\n",
            "Step=  354, Dmax= 1.8e-02 nm, Epot= -1.64776e+06 Fmax= 1.92091e+04, atom= 1703\rStep=  355, Dmax= 9.0e-03 nm, Epot= -1.64791e+06 Fmax= 5.95840e+03, atom= 1704\n",
            "Step=  356, Dmax= 1.1e-02 nm, Epot= -1.64806e+06 Fmax= 1.45999e+04, atom= 1703\n",
            "Step=  357, Dmax= 1.3e-02 nm, Epot= -1.64822e+06 Fmax= 9.76733e+03, atom= 1704\n",
            "Step=  358, Dmax= 1.6e-02 nm, Epot= -1.64828e+06 Fmax= 2.04325e+04, atom= 1704\n",
            "Step=  359, Dmax= 1.9e-02 nm, Epot= -1.64847e+06 Fmax= 1.41766e+04, atom= 1704\n",
            "Step=  360, Dmax= 2.2e-02 nm, Epot= -1.64838e+06 Fmax= 2.98348e+04, atom= 1704\rStep=  361, Dmax= 1.1e-02 nm, Epot= -1.64869e+06 Fmax= 4.51607e+03, atom= 1703\n",
            "Step=  362, Dmax= 1.3e-02 nm, Epot= -1.64882e+06 Fmax= 1.86778e+04, atom= 1703\n",
            "Step=  363, Dmax= 1.6e-02 nm, Epot= -1.64913e+06 Fmax= 9.66074e+03, atom= 1703\n",
            "Step=  364, Dmax= 1.9e-02 nm, Epot= -1.64906e+06 Fmax= 2.20629e+04, atom= 1703\rStep=  365, Dmax= 9.7e-03 nm, Epot= -1.64927e+06 Fmax= 8.22459e+03, atom= 1704\n",
            "Step=  366, Dmax= 1.2e-02 nm, Epot= -1.64939e+06 Fmax= 1.36847e+04, atom= 1703\n",
            "Step=  367, Dmax= 1.4e-02 nm, Epot= -1.64952e+06 Fmax= 1.18945e+04, atom= 1704\n",
            "Step=  368, Dmax= 1.7e-02 nm, Epot= -1.64959e+06 Fmax= 2.00621e+04, atom= 1703\n",
            "Step=  369, Dmax= 2.0e-02 nm, Epot= -1.64973e+06 Fmax= 1.62699e+04, atom= 1704\n",
            "Step=  370, Dmax= 2.4e-02 nm, Epot= -1.64965e+06 Fmax= 3.03161e+04, atom= 1704\rStep=  371, Dmax= 1.2e-02 nm, Epot= -1.65000e+06 Fmax= 3.26788e+03, atom= 1704\n",
            "Step=  372, Dmax= 1.5e-02 nm, Epot= -1.65017e+06 Fmax= 2.23559e+04, atom= 1703\n",
            "Step=  373, Dmax= 1.7e-02 nm, Epot= -1.65060e+06 Fmax= 8.14673e+03, atom= 1703\n",
            "Step=  374, Dmax= 2.1e-02 nm, Epot= -1.65047e+06 Fmax= 2.47253e+04, atom= 1703\rStep=  375, Dmax= 1.0e-02 nm, Epot= -1.65073e+06 Fmax= 1.04902e+04, atom= 1704\n",
            "Step=  376, Dmax= 1.3e-02 nm, Epot= -1.65085e+06 Fmax= 1.28470e+04, atom= 1703\n",
            "Step=  377, Dmax= 1.5e-02 nm, Epot= -1.65095e+06 Fmax= 1.40143e+04, atom= 1704\n",
            "Step=  378, Dmax= 1.8e-02 nm, Epot= -1.65103e+06 Fmax= 1.98373e+04, atom= 1703\n",
            "Step=  379, Dmax= 2.2e-02 nm, Epot= -1.65112e+06 Fmax= 1.83163e+04, atom= 1703\n",
            "Step=  380, Dmax= 2.6e-02 nm, Epot= -1.65107e+06 Fmax= 3.09765e+04, atom= 1704\rStep=  381, Dmax= 1.3e-02 nm, Epot= -1.65144e+06 Fmax= 2.29734e+03, atom= 1699\n",
            "Step=  382, Dmax= 1.6e-02 nm, Epot= -1.65174e+06 Fmax= 2.57831e+04, atom= 1703\n",
            "Step=  383, Dmax= 1.9e-02 nm, Epot= -1.65230e+06 Fmax= 8.85415e+03, atom= 1703\n",
            "Step=  384, Dmax= 2.2e-02 nm, Epot= -1.65213e+06 Fmax= 2.50365e+04, atom= 1703\rStep=  385, Dmax= 1.1e-02 nm, Epot= -1.65241e+06 Fmax= 1.10372e+04, atom= 1704\n",
            "Step=  386, Dmax= 1.3e-02 nm, Epot= -1.65252e+06 Fmax= 1.43536e+04, atom= 1703\n",
            "Step=  387, Dmax= 1.6e-02 nm, Epot= -1.65261e+06 Fmax= 1.46593e+04, atom= 1704\n",
            "Step=  388, Dmax= 1.9e-02 nm, Epot= -1.65267e+06 Fmax= 2.20535e+04, atom= 1704\n",
            "Step=  389, Dmax= 2.3e-02 nm, Epot= -1.65276e+06 Fmax= 1.90720e+04, atom= 1703\n",
            "Step=  390, Dmax= 2.8e-02 nm, Epot= -1.65264e+06 Fmax= 3.43157e+04, atom= 1704\rStep=  391, Dmax= 1.4e-02 nm, Epot= -1.65311e+06 Fmax= 2.73135e+03, atom= 1704\n",
            "Step=  392, Dmax= 1.7e-02 nm, Epot= -1.65318e+06 Fmax= 2.85085e+04, atom= 1703\n",
            "Step=  393, Dmax= 2.0e-02 nm, Epot= -1.65387e+06 Fmax= 7.58461e+03, atom= 1703\n",
            "Step=  394, Dmax= 2.4e-02 nm, Epot= -1.65362e+06 Fmax= 2.77971e+04, atom= 1703\rStep=  395, Dmax= 1.2e-02 nm, Epot= -1.65397e+06 Fmax= 1.29878e+04, atom= 1704\n",
            "Step=  396, Dmax= 1.4e-02 nm, Epot= -1.65410e+06 Fmax= 1.38110e+04, atom= 1703\n",
            "Step=  397, Dmax= 1.7e-02 nm, Epot= -1.65415e+06 Fmax= 1.66213e+04, atom= 1704\n",
            "Step=  398, Dmax= 2.1e-02 nm, Epot= -1.65423e+06 Fmax= 2.21836e+04, atom= 1703\n",
            "Step=  399, Dmax= 2.5e-02 nm, Epot= -1.65426e+06 Fmax= 2.10055e+04, atom= 1703\n",
            "Step=  400, Dmax= 3.0e-02 nm, Epot= -1.65417e+06 Fmax= 3.52904e+04, atom= 1704\rStep=  401, Dmax= 1.5e-02 nm, Epot= -1.65467e+06 Fmax= 2.72604e+03, atom= 1699\n",
            "Step=  402, Dmax= 1.8e-02 nm, Epot= -1.65500e+06 Fmax= 2.30379e+04, atom= 1703\n",
            "Step=  403, Dmax= 2.2e-02 nm, Epot= -1.65532e+06 Fmax= 2.11401e+04, atom= 1703\n",
            "Step=  404, Dmax= 2.6e-02 nm, Epot= -1.65524e+06 Fmax= 2.31506e+04, atom= 1704\rStep=  405, Dmax= 1.3e-02 nm, Epot= -1.65557e+06 Fmax= 5.63633e+03, atom= 1704\n",
            "Step=  406, Dmax= 1.6e-02 nm, Epot= -1.65561e+06 Fmax= 2.48688e+04, atom= 1704\n",
            "Step=  407, Dmax= 1.9e-02 nm, Epot= -1.65589e+06 Fmax= 1.15000e+04, atom= 1703\n",
            "Step=  408, Dmax= 2.2e-02 nm, Epot= -1.65566e+06 Fmax= 3.39291e+04, atom= 1703\rStep=  409, Dmax= 1.1e-02 nm, Epot= -1.65604e+06 Fmax= 7.98307e+03, atom= 1704\n",
            "Step=  410, Dmax= 1.3e-02 nm, Epot= -1.65609e+06 Fmax= 1.53849e+04, atom= 1703\n",
            "Step=  411, Dmax= 1.6e-02 nm, Epot= -1.65627e+06 Fmax= 1.37454e+04, atom= 1703\n",
            "Step=  412, Dmax= 1.9e-02 nm, Epot= -1.65624e+06 Fmax= 1.93028e+04, atom= 1703\rStep=  413, Dmax= 9.7e-03 nm, Epot= -1.65643e+06 Fmax= 4.97213e+03, atom= 1704\n",
            "Step=  414, Dmax= 1.2e-02 nm, Epot= -1.65654e+06 Fmax= 1.76338e+04, atom= 1704\n",
            "Step=  415, Dmax= 1.4e-02 nm, Epot= -1.65673e+06 Fmax= 9.14847e+03, atom= 1704\n",
            "Step=  416, Dmax= 1.7e-02 nm, Epot= -1.65669e+06 Fmax= 2.43252e+04, atom= 1704\rStep=  417, Dmax= 8.4e-03 nm, Epot= -1.65686e+06 Fmax= 5.73484e+03, atom= 1703\n",
            "Step=  418, Dmax= 1.0e-02 nm, Epot= -1.65696e+06 Fmax= 1.20538e+04, atom= 1704\n",
            "Step=  419, Dmax= 1.2e-02 nm, Epot= -1.65711e+06 Fmax= 9.86641e+03, atom= 1703\n",
            "Step=  420, Dmax= 1.4e-02 nm, Epot= -1.65715e+06 Fmax= 1.53520e+04, atom= 1703\n",
            "Step=  421, Dmax= 1.7e-02 nm, Epot= -1.65729e+06 Fmax= 1.65217e+04, atom= 1703\n",
            "Step=  422, Dmax= 2.1e-02 nm, Epot= -1.65729e+06 Fmax= 1.94097e+04, atom= 1703\rStep=  423, Dmax= 1.0e-02 nm, Epot= -1.65749e+06 Fmax= 4.03237e+03, atom= 1704\n",
            "Step=  424, Dmax= 1.2e-02 nm, Epot= -1.65762e+06 Fmax= 2.07602e+04, atom= 1704\n",
            "Step=  425, Dmax= 1.5e-02 nm, Epot= -1.65785e+06 Fmax= 8.72116e+03, atom= 1704\n",
            "Step=  426, Dmax= 1.8e-02 nm, Epot= -1.65774e+06 Fmax= 2.83860e+04, atom= 1704\rStep=  427, Dmax= 9.0e-03 nm, Epot= -1.65797e+06 Fmax= 7.65854e+03, atom= 1703\n",
            "Step=  428, Dmax= 1.1e-02 nm, Epot= -1.65806e+06 Fmax= 1.16510e+04, atom= 1704\n",
            "Step=  429, Dmax= 1.3e-02 nm, Epot= -1.65819e+06 Fmax= 1.22799e+04, atom= 1703\n",
            "Step=  430, Dmax= 1.6e-02 nm, Epot= -1.65823e+06 Fmax= 1.51980e+04, atom= 1704\n",
            "Step=  431, Dmax= 1.9e-02 nm, Epot= -1.65832e+06 Fmax= 1.95981e+04, atom= 1703\n",
            "Step=  432, Dmax= 2.2e-02 nm, Epot= -1.65835e+06 Fmax= 1.94834e+04, atom= 1703\n",
            "Step=  433, Dmax= 2.7e-02 nm, Epot= -1.65831e+06 Fmax= 3.09973e+04, atom= 1704\rStep=  434, Dmax= 1.3e-02 nm, Epot= -1.65870e+06 Fmax= 2.20639e+03, atom= 1699\n",
            "Step=  435, Dmax= 1.6e-02 nm, Epot= -1.65910e+06 Fmax= 2.11684e+04, atom= 1703\n",
            "Step=  436, Dmax= 1.9e-02 nm, Epot= -1.65939e+06 Fmax= 1.82890e+04, atom= 1703\n",
            "Step=  437, Dmax= 2.3e-02 nm, Epot= -1.65932e+06 Fmax= 2.15188e+04, atom= 1704\rStep=  438, Dmax= 1.2e-02 nm, Epot= -1.65959e+06 Fmax= 5.38382e+03, atom= 1704\n",
            "Step=  439, Dmax= 1.4e-02 nm, Epot= -1.65963e+06 Fmax= 2.20928e+04, atom= 1704\n",
            "Step=  440, Dmax= 1.7e-02 nm, Epot= -1.65987e+06 Fmax= 1.03743e+04, atom= 1703\n",
            "Step=  441, Dmax= 2.0e-02 nm, Epot= -1.65971e+06 Fmax= 3.01953e+04, atom= 1703\rStep=  442, Dmax= 1.0e-02 nm, Epot= -1.66000e+06 Fmax= 7.29802e+03, atom= 1704\n",
            "Step=  443, Dmax= 1.2e-02 nm, Epot= -1.66006e+06 Fmax= 1.38636e+04, atom= 1703\n",
            "Step=  444, Dmax= 1.4e-02 nm, Epot= -1.66021e+06 Fmax= 1.24158e+04, atom= 1703\n",
            "Step=  445, Dmax= 1.7e-02 nm, Epot= -1.66021e+06 Fmax= 1.75932e+04, atom= 1703\rStep=  446, Dmax= 8.7e-03 nm, Epot= -1.66036e+06 Fmax= 4.36432e+03, atom= 1704\n",
            "Step=  447, Dmax= 1.0e-02 nm, Epot= -1.66048e+06 Fmax= 1.58628e+04, atom= 1704\n",
            "Step=  448, Dmax= 1.2e-02 nm, Epot= -1.66064e+06 Fmax= 8.14010e+03, atom= 1704\n",
            "Step=  449, Dmax= 1.5e-02 nm, Epot= -1.66063e+06 Fmax= 2.17319e+04, atom= 1704\rStep=  450, Dmax= 7.5e-03 nm, Epot= -1.66075e+06 Fmax= 5.32159e+03, atom= 1703\n",
            "Step=  451, Dmax= 9.0e-03 nm, Epot= -1.66085e+06 Fmax= 1.07538e+04, atom= 1704\n",
            "Step=  452, Dmax= 1.1e-02 nm, Epot= -1.66098e+06 Fmax= 9.00505e+03, atom= 1703\n",
            "Step=  453, Dmax= 1.3e-02 nm, Epot= -1.66104e+06 Fmax= 1.38348e+04, atom= 1704\n",
            "Step=  454, Dmax= 1.6e-02 nm, Epot= -1.66116e+06 Fmax= 1.48691e+04, atom= 1703\n",
            "Step=  455, Dmax= 1.9e-02 nm, Epot= -1.66116e+06 Fmax= 1.77176e+04, atom= 1703\n",
            "Step=  456, Dmax= 2.2e-02 nm, Epot= -1.66122e+06 Fmax= 2.38980e+04, atom= 1703\n",
            "Step=  457, Dmax= 2.7e-02 nm, Epot= -1.66122e+06 Fmax= 2.22300e+04, atom= 1703\rStep=  458, Dmax= 1.3e-02 nm, Epot= -1.66156e+06 Fmax= 3.52907e+03, atom= 1703\n",
            "Step=  459, Dmax= 1.6e-02 nm, Epot= -1.66165e+06 Fmax= 2.90475e+04, atom= 1704\n",
            "Step=  460, Dmax= 1.9e-02 nm, Epot= -1.66200e+06 Fmax= 1.05073e+04, atom= 1704\n",
            "Step=  461, Dmax= 2.3e-02 nm, Epot= -1.66157e+06 Fmax= 4.05089e+04, atom= 1703\rStep=  462, Dmax= 1.2e-02 nm, Epot= -1.66210e+06 Fmax= 1.13992e+04, atom= 1703\n",
            "Step=  463, Dmax= 1.4e-02 nm, Epot= -1.66216e+06 Fmax= 1.34807e+04, atom= 1704\n",
            "Step=  464, Dmax= 1.7e-02 nm, Epot= -1.66224e+06 Fmax= 1.79035e+04, atom= 1703\n",
            "Step=  465, Dmax= 2.0e-02 nm, Epot= -1.66228e+06 Fmax= 1.75572e+04, atom= 1703\n",
            "Step=  466, Dmax= 2.4e-02 nm, Epot= -1.66225e+06 Fmax= 2.79914e+04, atom= 1704\rStep=  467, Dmax= 1.2e-02 nm, Epot= -1.66256e+06 Fmax= 1.91726e+03, atom= 1699\n",
            "Step=  468, Dmax= 1.4e-02 nm, Epot= -1.66286e+06 Fmax= 2.33565e+04, atom= 1703\n",
            "Step=  469, Dmax= 1.7e-02 nm, Epot= -1.66330e+06 Fmax= 9.47871e+03, atom= 1703\n",
            "Step=  470, Dmax= 2.1e-02 nm, Epot= -1.66314e+06 Fmax= 2.28644e+04, atom= 1703\rStep=  471, Dmax= 1.0e-02 nm, Epot= -1.66339e+06 Fmax= 9.43658e+03, atom= 1704\n",
            "Step=  472, Dmax= 1.2e-02 nm, Epot= -1.66345e+06 Fmax= 1.44541e+04, atom= 1703\n",
            "Step=  473, Dmax= 1.5e-02 nm, Epot= -1.66354e+06 Fmax= 1.29312e+04, atom= 1704\n",
            "Step=  474, Dmax= 1.8e-02 nm, Epot= -1.66355e+06 Fmax= 2.16020e+04, atom= 1704\n",
            "Step=  475, Dmax= 2.2e-02 nm, Epot= -1.66365e+06 Fmax= 1.72882e+04, atom= 1703\n",
            "Step=  476, Dmax= 2.6e-02 nm, Epot= -1.66351e+06 Fmax= 3.28754e+04, atom= 1704\rStep=  477, Dmax= 1.3e-02 nm, Epot= -1.66393e+06 Fmax= 3.53167e+03, atom= 1704\n",
            "Step=  478, Dmax= 1.5e-02 nm, Epot= -1.66391e+06 Fmax= 2.38175e+04, atom= 1703\rStep=  479, Dmax= 7.7e-03 nm, Epot= -1.66406e+06 Fmax= 1.10197e+04, atom= 1703\n",
            "Step=  480, Dmax= 9.3e-03 nm, Epot= -1.66420e+06 Fmax= 5.70862e+03, atom= 1703\n",
            "Step=  481, Dmax= 1.1e-02 nm, Epot= -1.66427e+06 Fmax= 1.36167e+04, atom= 1704\n",
            "Step=  482, Dmax= 1.3e-02 nm, Epot= -1.66442e+06 Fmax= 1.06757e+04, atom= 1703\n",
            "Step=  483, Dmax= 1.6e-02 nm, Epot= -1.66440e+06 Fmax= 1.70899e+04, atom= 1703\rStep=  484, Dmax= 8.0e-03 nm, Epot= -1.66454e+06 Fmax= 4.72459e+03, atom= 1704\n",
            "Step=  485, Dmax= 9.6e-03 nm, Epot= -1.66463e+06 Fmax= 1.38607e+04, atom= 1704\n",
            "Step=  486, Dmax= 1.2e-02 nm, Epot= -1.66477e+06 Fmax= 8.16023e+03, atom= 1704\n",
            "Step=  487, Dmax= 1.4e-02 nm, Epot= -1.66478e+06 Fmax= 1.91233e+04, atom= 1704\n",
            "Step=  488, Dmax= 1.7e-02 nm, Epot= -1.66494e+06 Fmax= 1.22418e+04, atom= 1704\n",
            "Step=  489, Dmax= 2.0e-02 nm, Epot= -1.66483e+06 Fmax= 2.74690e+04, atom= 1704\rStep=  490, Dmax= 1.0e-02 nm, Epot= -1.66509e+06 Fmax= 4.95531e+03, atom= 1704\n",
            "Step=  491, Dmax= 1.2e-02 nm, Epot= -1.66514e+06 Fmax= 1.59577e+04, atom= 1703\n",
            "Step=  492, Dmax= 1.4e-02 nm, Epot= -1.66535e+06 Fmax= 9.68930e+03, atom= 1703\n",
            "Step=  493, Dmax= 1.7e-02 nm, Epot= -1.66528e+06 Fmax= 1.94698e+04, atom= 1703\rStep=  494, Dmax= 8.6e-03 nm, Epot= -1.66545e+06 Fmax= 6.53432e+03, atom= 1704\n",
            "Step=  495, Dmax= 1.0e-02 nm, Epot= -1.66553e+06 Fmax= 1.32391e+04, atom= 1703\n",
            "Step=  496, Dmax= 1.2e-02 nm, Epot= -1.66564e+06 Fmax= 9.96560e+03, atom= 1704\n",
            "Step=  497, Dmax= 1.5e-02 nm, Epot= -1.66566e+06 Fmax= 1.89270e+04, atom= 1703\n",
            "Step=  498, Dmax= 1.8e-02 nm, Epot= -1.66577e+06 Fmax= 1.41094e+04, atom= 1704\n",
            "Step=  499, Dmax= 2.1e-02 nm, Epot= -1.66567e+06 Fmax= 2.79808e+04, atom= 1704\rStep=  500, Dmax= 1.1e-02 nm, Epot= -1.66597e+06 Fmax= 3.91674e+03, atom= 1704\n",
            "Step=  501, Dmax= 1.3e-02 nm, Epot= -1.66601e+06 Fmax= 1.86057e+04, atom= 1703\n",
            "Step=  502, Dmax= 1.5e-02 nm, Epot= -1.66630e+06 Fmax= 8.68516e+03, atom= 1703\n",
            "Step=  503, Dmax= 1.9e-02 nm, Epot= -1.66616e+06 Fmax= 2.18484e+04, atom= 1703\rStep=  504, Dmax= 9.3e-03 nm, Epot= -1.66639e+06 Fmax= 8.37427e+03, atom= 1703\n",
            "Step=  505, Dmax= 1.1e-02 nm, Epot= -1.66646e+06 Fmax= 1.26720e+04, atom= 1703\n",
            "Step=  506, Dmax= 1.3e-02 nm, Epot= -1.66654e+06 Fmax= 1.17729e+04, atom= 1704\n",
            "Step=  507, Dmax= 1.6e-02 nm, Epot= -1.66657e+06 Fmax= 1.88605e+04, atom= 1703\n",
            "Step=  508, Dmax= 1.9e-02 nm, Epot= -1.66666e+06 Fmax= 1.59579e+04, atom= 1703\n",
            "Step=  509, Dmax= 2.3e-02 nm, Epot= -1.66657e+06 Fmax= 2.86013e+04, atom= 1704\rStep=  510, Dmax= 1.2e-02 nm, Epot= -1.66689e+06 Fmax= 2.92355e+03, atom= 1704\n",
            "Step=  511, Dmax= 1.4e-02 nm, Epot= -1.66695e+06 Fmax= 2.19229e+04, atom= 1703\n",
            "Step=  512, Dmax= 1.7e-02 nm, Epot= -1.66734e+06 Fmax= 7.49807e+03, atom= 1703\n",
            "Step=  513, Dmax= 2.0e-02 nm, Epot= -1.66714e+06 Fmax= 2.41072e+04, atom= 1703\rStep=  514, Dmax= 1.0e-02 nm, Epot= -1.66741e+06 Fmax= 1.02988e+04, atom= 1704\n",
            "Step=  515, Dmax= 1.2e-02 nm, Epot= -1.66750e+06 Fmax= 1.21289e+04, atom= 1703\n",
            "Step=  516, Dmax= 1.4e-02 nm, Epot= -1.66755e+06 Fmax= 1.36188e+04, atom= 1704\n",
            "Step=  517, Dmax= 1.7e-02 nm, Epot= -1.66760e+06 Fmax= 1.88988e+04, atom= 1703\n",
            "Step=  518, Dmax= 2.1e-02 nm, Epot= -1.66764e+06 Fmax= 1.78177e+04, atom= 1703\n",
            "Step=  519, Dmax= 2.5e-02 nm, Epot= -1.66757e+06 Fmax= 2.93571e+04, atom= 1703\rStep=  520, Dmax= 1.2e-02 nm, Epot= -1.66793e+06 Fmax= 2.12145e+03, atom= 1699\n",
            "Step=  521, Dmax= 1.5e-02 nm, Epot= -1.66804e+06 Fmax= 2.50222e+04, atom= 1703\n",
            "Step=  522, Dmax= 1.8e-02 nm, Epot= -1.66855e+06 Fmax= 8.18105e+03, atom= 1703\n",
            "Step=  523, Dmax= 2.1e-02 nm, Epot= -1.66833e+06 Fmax= 2.43583e+04, atom= 1703\rStep=  524, Dmax= 1.1e-02 nm, Epot= -1.66861e+06 Fmax= 1.07655e+04, atom= 1704\n",
            "Step=  525, Dmax= 1.3e-02 nm, Epot= -1.66869e+06 Fmax= 1.35810e+04, atom= 1703\n",
            "Step=  526, Dmax= 1.5e-02 nm, Epot= -1.66874e+06 Fmax= 1.42020e+04, atom= 1704\n",
            "Step=  527, Dmax= 1.9e-02 nm, Epot= -1.66876e+06 Fmax= 2.10206e+04, atom= 1703\n",
            "Step=  528, Dmax= 2.2e-02 nm, Epot= -1.66881e+06 Fmax= 1.85244e+04, atom= 1703\n",
            "Step=  529, Dmax= 2.7e-02 nm, Epot= -1.66868e+06 Fmax= 3.25165e+04, atom= 1703\rStep=  530, Dmax= 1.3e-02 nm, Epot= -1.66912e+06 Fmax= 2.57739e+03, atom= 1704\n",
            "Step=  531, Dmax= 1.6e-02 nm, Epot= -1.66906e+06 Fmax= 2.74268e+04, atom= 1703\rStep=  532, Dmax= 8.0e-03 nm, Epot= -1.66927e+06 Fmax= 1.29945e+04, atom= 1703\n",
            "Step=  533, Dmax= 9.6e-03 nm, Epot= -1.66943e+06 Fmax= 4.42416e+03, atom= 1703\n",
            "Step=  534, Dmax= 1.2e-02 nm, Epot= -1.66950e+06 Fmax= 1.48464e+04, atom= 1704\n",
            "Step=  535, Dmax= 1.4e-02 nm, Epot= -1.66967e+06 Fmax= 9.85997e+03, atom= 1703\n",
            "Step=  536, Dmax= 1.7e-02 nm, Epot= -1.66961e+06 Fmax= 1.84903e+04, atom= 1703\rStep=  537, Dmax= 8.3e-03 nm, Epot= -1.66978e+06 Fmax= 5.86579e+03, atom= 1703\n",
            "Step=  538, Dmax= 1.0e-02 nm, Epot= -1.66984e+06 Fmax= 1.31868e+04, atom= 1703\n",
            "Step=  539, Dmax= 1.2e-02 nm, Epot= -1.66995e+06 Fmax= 9.25285e+03, atom= 1704\n",
            "Step=  540, Dmax= 1.4e-02 nm, Epot= -1.66995e+06 Fmax= 1.86480e+04, atom= 1703\n",
            "Step=  541, Dmax= 1.7e-02 nm, Epot= -1.67008e+06 Fmax= 1.33185e+04, atom= 1704\n",
            "Step=  542, Dmax= 2.1e-02 nm, Epot= -1.66997e+06 Fmax= 2.73111e+04, atom= 1704\rStep=  543, Dmax= 1.0e-02 nm, Epot= -1.67025e+06 Fmax= 4.18692e+03, atom= 1704\n",
            "Step=  544, Dmax= 1.2e-02 nm, Epot= -1.67028e+06 Fmax= 1.74703e+04, atom= 1703\n",
            "Step=  545, Dmax= 1.5e-02 nm, Epot= -1.67052e+06 Fmax= 8.84459e+03, atom= 1703\n",
            "Step=  546, Dmax= 1.8e-02 nm, Epot= -1.67040e+06 Fmax= 2.08326e+04, atom= 1703\rStep=  547, Dmax= 8.9e-03 nm, Epot= -1.67061e+06 Fmax= 7.67886e+03, atom= 1703\n",
            "Step=  548, Dmax= 1.1e-02 nm, Epot= -1.67067e+06 Fmax= 1.26174e+04, atom= 1703\n",
            "Step=  549, Dmax= 1.3e-02 nm, Epot= -1.67075e+06 Fmax= 1.10322e+04, atom= 1704\n",
            "Step=  550, Dmax= 1.5e-02 nm, Epot= -1.67077e+06 Fmax= 1.85608e+04, atom= 1703\n",
            "Step=  551, Dmax= 1.8e-02 nm, Epot= -1.67086e+06 Fmax= 1.51538e+04, atom= 1703\n",
            "Step=  552, Dmax= 2.2e-02 nm, Epot= -1.67076e+06 Fmax= 2.78808e+04, atom= 1703\rStep=  553, Dmax= 1.1e-02 nm, Epot= -1.67107e+06 Fmax= 3.19652e+03, atom= 1704\n",
            "Step=  554, Dmax= 1.3e-02 nm, Epot= -1.67109e+06 Fmax= 2.04543e+04, atom= 1703\n",
            "Step=  555, Dmax= 1.6e-02 nm, Epot= -1.67143e+06 Fmax= 7.75457e+03, atom= 1703\n",
            "Step=  556, Dmax= 1.9e-02 nm, Epot= -1.67125e+06 Fmax= 2.31607e+04, atom= 1703\rStep=  557, Dmax= 9.6e-03 nm, Epot= -1.67150e+06 Fmax= 9.55393e+03, atom= 1703\n",
            "Step=  558, Dmax= 1.2e-02 nm, Epot= -1.67158e+06 Fmax= 1.20716e+04, atom= 1703\n",
            "Step=  559, Dmax= 1.4e-02 nm, Epot= -1.67163e+06 Fmax= 1.28465e+04, atom= 1703\n",
            "Step=  560, Dmax= 1.7e-02 nm, Epot= -1.67167e+06 Fmax= 1.85631e+04, atom= 1703\n",
            "Step=  561, Dmax= 2.0e-02 nm, Epot= -1.67172e+06 Fmax= 1.70029e+04, atom= 1703\n",
            "Step=  562, Dmax= 2.4e-02 nm, Epot= -1.67163e+06 Fmax= 2.85707e+04, atom= 1703\rStep=  563, Dmax= 1.2e-02 nm, Epot= -1.67197e+06 Fmax= 2.23154e+03, atom= 1704\n",
            "Step=  564, Dmax= 1.4e-02 nm, Epot= -1.67200e+06 Fmax= 2.47103e+04, atom= 1703\n",
            "Step=  565, Dmax= 1.7e-02 nm, Epot= -1.67250e+06 Fmax= 6.26652e+03, atom= 1703\n",
            "Step=  566, Dmax= 2.1e-02 nm, Epot= -1.67228e+06 Fmax= 2.47789e+04, atom= 1703\rStep=  567, Dmax= 1.0e-02 nm, Epot= -1.67256e+06 Fmax= 1.14417e+04, atom= 1704\n",
            "Step=  568, Dmax= 1.2e-02 nm, Epot= -1.67265e+06 Fmax= 1.15910e+04, atom= 1703\n",
            "Step=  569, Dmax= 1.5e-02 nm, Epot= -1.67267e+06 Fmax= 1.47273e+04, atom= 1703\n",
            "Step=  570, Dmax= 1.8e-02 nm, Epot= -1.67274e+06 Fmax= 1.86031e+04, atom= 1703\n",
            "Step=  571, Dmax= 2.1e-02 nm, Epot= -1.67274e+06 Fmax= 1.89140e+04, atom= 1703\n",
            "Step=  572, Dmax= 2.6e-02 nm, Epot= -1.67268e+06 Fmax= 2.93538e+04, atom= 1703\rStep=  573, Dmax= 1.3e-02 nm, Epot= -1.67305e+06 Fmax= 2.01385e+03, atom= 1699\n",
            "Step=  574, Dmax= 1.5e-02 nm, Epot= -1.67331e+06 Fmax= 2.02732e+04, atom= 1703\n",
            "Step=  575, Dmax= 1.8e-02 nm, Epot= -1.67355e+06 Fmax= 1.74820e+04, atom= 1703\n",
            "Step=  576, Dmax= 2.2e-02 nm, Epot= -1.67347e+06 Fmax= 2.06742e+04, atom= 1704\rStep=  577, Dmax= 1.1e-02 nm, Epot= -1.67373e+06 Fmax= 5.09587e+03, atom= 1704\n",
            "Step=  578, Dmax= 1.3e-02 nm, Epot= -1.67372e+06 Fmax= 2.11812e+04, atom= 1704\rStep=  579, Dmax= 6.6e-03 nm, Epot= -1.67381e+06 Fmax= 7.14051e+03, atom= 1704\n",
            "Step=  580, Dmax= 8.0e-03 nm, Epot= -1.67389e+06 Fmax= 7.59274e+03, atom= 1704\n",
            "Step=  581, Dmax= 9.6e-03 nm, Epot= -1.67395e+06 Fmax= 1.05595e+04, atom= 1703\n",
            "Step=  582, Dmax= 1.1e-02 nm, Epot= -1.67402e+06 Fmax= 1.05110e+04, atom= 1704\n",
            "Step=  583, Dmax= 1.4e-02 nm, Epot= -1.67406e+06 Fmax= 1.58088e+04, atom= 1703\n",
            "Step=  584, Dmax= 1.7e-02 nm, Epot= -1.67412e+06 Fmax= 1.42803e+04, atom= 1703\n",
            "Step=  585, Dmax= 2.0e-02 nm, Epot= -1.67409e+06 Fmax= 2.39093e+04, atom= 1703\rStep=  586, Dmax= 9.9e-03 nm, Epot= -1.67431e+06 Fmax= 2.31687e+03, atom= 1703\n",
            "Step=  587, Dmax= 1.2e-02 nm, Epot= -1.67442e+06 Fmax= 1.93138e+04, atom= 1703\n",
            "Step=  588, Dmax= 1.4e-02 nm, Epot= -1.67473e+06 Fmax= 6.23523e+03, atom= 1703\n",
            "Step=  589, Dmax= 1.7e-02 nm, Epot= -1.67460e+06 Fmax= 2.14019e+04, atom= 1703\rStep=  590, Dmax= 8.6e-03 nm, Epot= -1.67479e+06 Fmax= 9.12397e+03, atom= 1704\n",
            "Step=  591, Dmax= 1.0e-02 nm, Epot= -1.67487e+06 Fmax= 1.02135e+04, atom= 1703\n",
            "Step=  592, Dmax= 1.2e-02 nm, Epot= -1.67492e+06 Fmax= 1.20809e+04, atom= 1703\n",
            "Step=  593, Dmax= 1.5e-02 nm, Epot= -1.67497e+06 Fmax= 1.59099e+04, atom= 1703\n",
            "Step=  594, Dmax= 1.8e-02 nm, Epot= -1.67500e+06 Fmax= 1.59582e+04, atom= 1703\n",
            "Step=  595, Dmax= 2.1e-02 nm, Epot= -1.67498e+06 Fmax= 2.46028e+04, atom= 1703\rStep=  596, Dmax= 1.1e-02 nm, Epot= -1.67523e+06 Fmax= 1.59866e+03, atom= 1699\n",
            "Step=  597, Dmax= 1.3e-02 nm, Epot= -1.67543e+06 Fmax= 2.24175e+04, atom= 1703\n",
            "Step=  598, Dmax= 1.5e-02 nm, Epot= -1.67583e+06 Fmax= 6.21147e+03, atom= 1703\n",
            "Step=  599, Dmax= 1.8e-02 nm, Epot= -1.67570e+06 Fmax= 2.17701e+04, atom= 1703\rStep=  600, Dmax= 9.2e-03 nm, Epot= -1.67589e+06 Fmax= 9.85437e+03, atom= 1704\n",
            "Step=  601, Dmax= 1.1e-02 nm, Epot= -1.67597e+06 Fmax= 1.09967e+04, atom= 1703\n",
            "Step=  602, Dmax= 1.3e-02 nm, Epot= -1.67601e+06 Fmax= 1.29312e+04, atom= 1703\n",
            "Step=  603, Dmax= 1.6e-02 nm, Epot= -1.67605e+06 Fmax= 1.72476e+04, atom= 1703\n",
            "Step=  604, Dmax= 1.9e-02 nm, Epot= -1.67608e+06 Fmax= 1.69323e+04, atom= 1703\n",
            "Step=  605, Dmax= 2.3e-02 nm, Epot= -1.67603e+06 Fmax= 2.67251e+04, atom= 1703\rStep=  606, Dmax= 1.1e-02 nm, Epot= -1.67632e+06 Fmax= 1.80848e+03, atom= 1699\n",
            "Step=  607, Dmax= 1.4e-02 nm, Epot= -1.67645e+06 Fmax= 2.34668e+04, atom= 1703\n",
            "Step=  608, Dmax= 1.7e-02 nm, Epot= -1.67689e+06 Fmax= 7.44408e+03, atom= 1703\n",
            "Step=  609, Dmax= 2.0e-02 nm, Epot= -1.67669e+06 Fmax= 2.28775e+04, atom= 1703\rStep=  610, Dmax= 9.9e-03 nm, Epot= -1.67694e+06 Fmax= 1.00728e+04, atom= 1704\n",
            "Step=  611, Dmax= 1.2e-02 nm, Epot= -1.67700e+06 Fmax= 1.25209e+04, atom= 1703\n",
            "Step=  612, Dmax= 1.4e-02 nm, Epot= -1.67704e+06 Fmax= 1.32971e+04, atom= 1703\n",
            "Step=  613, Dmax= 1.7e-02 nm, Epot= -1.67706e+06 Fmax= 1.93781e+04, atom= 1703\n",
            "Step=  614, Dmax= 2.1e-02 nm, Epot= -1.67710e+06 Fmax= 1.74738e+04, atom= 1703\n",
            "Step=  615, Dmax= 2.5e-02 nm, Epot= -1.67699e+06 Fmax= 2.97920e+04, atom= 1703\rStep=  616, Dmax= 1.2e-02 nm, Epot= -1.67736e+06 Fmax= 2.39028e+03, atom= 1704\n",
            "Step=  617, Dmax= 1.5e-02 nm, Epot= -1.67731e+06 Fmax= 2.53014e+04, atom= 1703\rStep=  618, Dmax= 7.4e-03 nm, Epot= -1.67749e+06 Fmax= 1.20241e+04, atom= 1703\n",
            "Step=  619, Dmax= 8.9e-03 nm, Epot= -1.67763e+06 Fmax= 4.14630e+03, atom= 1703\n",
            "Step=  620, Dmax= 1.1e-02 nm, Epot= -1.67768e+06 Fmax= 1.38481e+04, atom= 1704\n",
            "Step=  621, Dmax= 1.3e-02 nm, Epot= -1.67783e+06 Fmax= 9.16594e+03, atom= 1703\n",
            "Step=  622, Dmax= 1.5e-02 nm, Epot= -1.67777e+06 Fmax= 1.73195e+04, atom= 1703\rStep=  623, Dmax= 7.7e-03 nm, Epot= -1.67791e+06 Fmax= 5.41047e+03, atom= 1703\n",
            "Step=  624, Dmax= 9.2e-03 nm, Epot= -1.67797e+06 Fmax= 1.22245e+04, atom= 1703\n",
            "Step=  625, Dmax= 1.1e-02 nm, Epot= -1.67806e+06 Fmax= 8.55793e+03, atom= 1704\n",
            "Step=  626, Dmax= 1.3e-02 nm, Epot= -1.67806e+06 Fmax= 1.72887e+04, atom= 1703\rStep=  627, Dmax= 6.6e-03 nm, Epot= -1.67815e+06 Fmax= 3.22466e+03, atom= 1703\n",
            "Step=  628, Dmax= 8.0e-03 nm, Epot= -1.67824e+06 Fmax= 1.10206e+04, atom= 1703\n",
            "Step=  629, Dmax= 9.5e-03 nm, Epot= -1.67836e+06 Fmax= 6.34020e+03, atom= 1703\n",
            "Step=  630, Dmax= 1.1e-02 nm, Epot= -1.67837e+06 Fmax= 1.37280e+04, atom= 1703\n",
            "Step=  631, Dmax= 1.4e-02 nm, Epot= -1.67850e+06 Fmax= 1.13917e+04, atom= 1703\n",
            "Step=  632, Dmax= 1.6e-02 nm, Epot= -1.67845e+06 Fmax= 1.73155e+04, atom= 1703\rStep=  633, Dmax= 8.2e-03 nm, Epot= -1.67861e+06 Fmax= 4.53696e+03, atom= 1703\n",
            "Step=  634, Dmax= 9.9e-03 nm, Epot= -1.67866e+06 Fmax= 1.47291e+04, atom= 1704\n",
            "Step=  635, Dmax= 1.2e-02 nm, Epot= -1.67878e+06 Fmax= 8.04416e+03, atom= 1704\n",
            "Step=  636, Dmax= 1.4e-02 nm, Epot= -1.67873e+06 Fmax= 2.03629e+04, atom= 1703\rStep=  637, Dmax= 7.1e-03 nm, Epot= -1.67887e+06 Fmax= 4.80795e+03, atom= 1703\n",
            "Step=  638, Dmax= 8.5e-03 nm, Epot= -1.67892e+06 Fmax= 1.05532e+04, atom= 1703\n",
            "Step=  639, Dmax= 1.0e-02 nm, Epot= -1.67902e+06 Fmax= 8.29750e+03, atom= 1703\n",
            "Step=  640, Dmax= 1.2e-02 nm, Epot= -1.67904e+06 Fmax= 1.35351e+04, atom= 1703\n",
            "Step=  641, Dmax= 1.5e-02 nm, Epot= -1.67913e+06 Fmax= 1.37926e+04, atom= 1703\n",
            "Step=  642, Dmax= 1.8e-02 nm, Epot= -1.67910e+06 Fmax= 1.73534e+04, atom= 1703\rStep=  643, Dmax= 8.9e-03 nm, Epot= -1.67926e+06 Fmax= 3.64574e+03, atom= 1703\n",
            "Step=  644, Dmax= 1.1e-02 nm, Epot= -1.67932e+06 Fmax= 1.73515e+04, atom= 1704\n",
            "Step=  645, Dmax= 1.3e-02 nm, Epot= -1.67948e+06 Fmax= 7.59773e+03, atom= 1704\n",
            "Step=  646, Dmax= 1.5e-02 nm, Epot= -1.67938e+06 Fmax= 2.37118e+04, atom= 1703\rStep=  647, Dmax= 7.7e-03 nm, Epot= -1.67956e+06 Fmax= 6.47584e+03, atom= 1703\n",
            "Step=  648, Dmax= 9.2e-03 nm, Epot= -1.67961e+06 Fmax= 1.01406e+04, atom= 1703\n",
            "Step=  649, Dmax= 1.1e-02 nm, Epot= -1.67968e+06 Fmax= 1.04003e+04, atom= 1703\n",
            "Step=  650, Dmax= 1.3e-02 nm, Epot= -1.67970e+06 Fmax= 1.33341e+04, atom= 1703\n",
            "Step=  651, Dmax= 1.6e-02 nm, Epot= -1.67976e+06 Fmax= 1.64451e+04, atom= 1703\n",
            "Step=  652, Dmax= 1.9e-02 nm, Epot= -1.67976e+06 Fmax= 1.73810e+04, atom= 1703\n",
            "Step=  653, Dmax= 2.3e-02 nm, Epot= -1.67973e+06 Fmax= 2.57649e+04, atom= 1703\rStep=  654, Dmax= 1.1e-02 nm, Epot= -1.68002e+06 Fmax= 1.62587e+03, atom= 1699\n",
            "Step=  655, Dmax= 1.4e-02 nm, Epot= -1.68030e+06 Fmax= 1.86876e+04, atom= 1703\n",
            "Step=  656, Dmax= 1.6e-02 nm, Epot= -1.68052e+06 Fmax= 1.47897e+04, atom= 1703\n",
            "Step=  657, Dmax= 2.0e-02 nm, Epot= -1.68044e+06 Fmax= 1.91769e+04, atom= 1704\rStep=  658, Dmax= 9.9e-03 nm, Epot= -1.68065e+06 Fmax= 5.02006e+03, atom= 1704\n",
            "Step=  659, Dmax= 1.2e-02 nm, Epot= -1.68065e+06 Fmax= 1.85464e+04, atom= 1704\rStep=  660, Dmax= 5.9e-03 nm, Epot= -1.68072e+06 Fmax= 6.08894e+03, atom= 1703\n",
            "Step=  661, Dmax= 7.1e-03 nm, Epot= -1.68078e+06 Fmax= 7.01900e+03, atom= 1704\n",
            "Step=  662, Dmax= 8.5e-03 nm, Epot= -1.68085e+06 Fmax= 9.20395e+03, atom= 1703\n",
            "Step=  663, Dmax= 1.0e-02 nm, Epot= -1.68091e+06 Fmax= 9.62129e+03, atom= 1703\n",
            "Step=  664, Dmax= 1.2e-02 nm, Epot= -1.68095e+06 Fmax= 1.38601e+04, atom= 1703\n",
            "Step=  665, Dmax= 1.5e-02 nm, Epot= -1.68100e+06 Fmax= 1.31022e+04, atom= 1703\n",
            "Step=  666, Dmax= 1.8e-02 nm, Epot= -1.68098e+06 Fmax= 2.08851e+04, atom= 1703\rStep=  667, Dmax= 8.8e-03 nm, Epot= -1.68116e+06 Fmax= 1.92226e+03, atom= 1703\n",
            "Step=  668, Dmax= 1.1e-02 nm, Epot= -1.68128e+06 Fmax= 1.75720e+04, atom= 1703\n",
            "Step=  669, Dmax= 1.3e-02 nm, Epot= -1.68153e+06 Fmax= 5.37814e+03, atom= 1703\n",
            "Step=  670, Dmax= 1.5e-02 nm, Epot= -1.68145e+06 Fmax= 1.95557e+04, atom= 1703\rStep=  671, Dmax= 7.6e-03 nm, Epot= -1.68160e+06 Fmax= 8.33323e+03, atom= 1704\n",
            "Step=  672, Dmax= 9.2e-03 nm, Epot= -1.68167e+06 Fmax= 8.95523e+03, atom= 1703\n",
            "Step=  673, Dmax= 1.1e-02 nm, Epot= -1.68171e+06 Fmax= 1.10364e+04, atom= 1703\n",
            "Step=  674, Dmax= 1.3e-02 nm, Epot= -1.68176e+06 Fmax= 1.39282e+04, atom= 1703\n",
            "Step=  675, Dmax= 1.6e-02 nm, Epot= -1.68178e+06 Fmax= 1.46703e+04, atom= 1703\n",
            "Step=  676, Dmax= 1.9e-02 nm, Epot= -1.68178e+06 Fmax= 2.14758e+04, atom= 1703\rStep=  677, Dmax= 9.5e-03 nm, Epot= -1.68197e+06 Fmax= 1.27059e+03, atom= 1699\n",
            "Step=  678, Dmax= 1.1e-02 nm, Epot= -1.68223e+06 Fmax= 2.01343e+04, atom= 1703\n",
            "Step=  679, Dmax= 1.4e-02 nm, Epot= -1.68255e+06 Fmax= 5.65525e+03, atom= 1703\n",
            "Step=  680, Dmax= 1.6e-02 nm, Epot= -1.68246e+06 Fmax= 1.96557e+04, atom= 1703\rStep=  681, Dmax= 8.2e-03 nm, Epot= -1.68261e+06 Fmax= 8.74761e+03, atom= 1704\n",
            "Step=  682, Dmax= 9.9e-03 nm, Epot= -1.68267e+06 Fmax= 9.94533e+03, atom= 1703\n",
            "Step=  683, Dmax= 1.2e-02 nm, Epot= -1.68271e+06 Fmax= 1.15838e+04, atom= 1703\n",
            "Step=  684, Dmax= 1.4e-02 nm, Epot= -1.68275e+06 Fmax= 1.54291e+04, atom= 1703\n",
            "Step=  685, Dmax= 1.7e-02 nm, Epot= -1.68278e+06 Fmax= 1.53628e+04, atom= 1703\n",
            "Step=  686, Dmax= 2.0e-02 nm, Epot= -1.68274e+06 Fmax= 2.36822e+04, atom= 1703\rStep=  687, Dmax= 1.0e-02 nm, Epot= -1.68298e+06 Fmax= 1.58854e+03, atom= 1704\n",
            "Step=  688, Dmax= 1.2e-02 nm, Epot= -1.68309e+06 Fmax= 2.20949e+04, atom= 1703\n",
            "Step=  689, Dmax= 1.5e-02 nm, Epot= -1.68348e+06 Fmax= 4.89728e+03, atom= 1703\n",
            "Step=  690, Dmax= 1.8e-02 nm, Epot= -1.68336e+06 Fmax= 2.16841e+04, atom= 1703\rStep=  691, Dmax= 8.8e-03 nm, Epot= -1.68354e+06 Fmax= 1.01627e+04, atom= 1704\n",
            "Step=  692, Dmax= 1.1e-02 nm, Epot= -1.68361e+06 Fmax= 9.60848e+03, atom= 1703\n",
            "Step=  693, Dmax= 1.3e-02 nm, Epot= -1.68363e+06 Fmax= 1.32027e+04, atom= 1703\n",
            "Step=  694, Dmax= 1.5e-02 nm, Epot= -1.68369e+06 Fmax= 1.54056e+04, atom= 1703\n",
            "Step=  695, Dmax= 1.8e-02 nm, Epot= -1.68367e+06 Fmax= 1.71273e+04, atom= 1703\rStep=  696, Dmax= 9.2e-03 nm, Epot= -1.68384e+06 Fmax= 2.89160e+03, atom= 1703\n",
            "Step=  697, Dmax= 1.1e-02 nm, Epot= -1.68390e+06 Fmax= 1.89774e+04, atom= 1704\n",
            "Step=  698, Dmax= 1.3e-02 nm, Epot= -1.68408e+06 Fmax= 7.20575e+03, atom= 1704\n",
            "Step=  699, Dmax= 1.6e-02 nm, Epot= -1.68394e+06 Fmax= 2.58856e+04, atom= 1703\rStep=  700, Dmax= 7.9e-03 nm, Epot= -1.68415e+06 Fmax= 7.64747e+03, atom= 1703\n",
            "Step=  701, Dmax= 9.5e-03 nm, Epot= -1.68420e+06 Fmax= 9.67009e+03, atom= 1703\n",
            "Step=  702, Dmax= 1.1e-02 nm, Epot= -1.68425e+06 Fmax= 1.18486e+04, atom= 1703\n",
            "Step=  703, Dmax= 1.4e-02 nm, Epot= -1.68428e+06 Fmax= 1.29598e+04, atom= 1703\n",
            "Step=  704, Dmax= 1.6e-02 nm, Epot= -1.68430e+06 Fmax= 1.81981e+04, atom= 1703\n",
            "Step=  705, Dmax= 2.0e-02 nm, Epot= -1.68432e+06 Fmax= 1.71469e+04, atom= 1703\n",
            "Step=  706, Dmax= 2.4e-02 nm, Epot= -1.68423e+06 Fmax= 2.79895e+04, atom= 1703\rStep=  707, Dmax= 1.2e-02 nm, Epot= -1.68457e+06 Fmax= 2.00007e+03, atom= 1704\n",
            "Step=  708, Dmax= 1.4e-02 nm, Epot= -1.68451e+06 Fmax= 2.52721e+04, atom= 1703\rStep=  709, Dmax= 7.1e-03 nm, Epot= -1.68469e+06 Fmax= 1.20746e+04, atom= 1703\n",
            "Step=  710, Dmax= 8.5e-03 nm, Epot= -1.68482e+06 Fmax= 3.55365e+03, atom= 1703\n",
            "Step=  711, Dmax= 1.0e-02 nm, Epot= -1.68487e+06 Fmax= 1.34929e+04, atom= 1704\n",
            "Step=  712, Dmax= 1.2e-02 nm, Epot= -1.68500e+06 Fmax= 8.48641e+03, atom= 1703\n",
            "Step=  713, Dmax= 1.5e-02 nm, Epot= -1.68494e+06 Fmax= 1.70231e+04, atom= 1703\rStep=  714, Dmax= 7.3e-03 nm, Epot= -1.68507e+06 Fmax= 5.48877e+03, atom= 1703\n",
            "Step=  715, Dmax= 8.8e-03 nm, Epot= -1.68512e+06 Fmax= 1.13256e+04, atom= 1703\n",
            "Step=  716, Dmax= 1.1e-02 nm, Epot= -1.68519e+06 Fmax= 8.52208e+03, atom= 1703\n",
            "Step=  717, Dmax= 1.3e-02 nm, Epot= -1.68519e+06 Fmax= 1.61707e+04, atom= 1703\rStep=  718, Dmax= 6.3e-03 nm, Epot= -1.68528e+06 Fmax= 2.77465e+03, atom= 1703\n",
            "Step=  719, Dmax= 7.6e-03 nm, Epot= -1.68536e+06 Fmax= 1.09450e+04, atom= 1703\n",
            "Step=  720, Dmax= 9.1e-03 nm, Epot= -1.68547e+06 Fmax= 5.69659e+03, atom= 1703\n",
            "Step=  721, Dmax= 1.1e-02 nm, Epot= -1.68548e+06 Fmax= 1.35436e+04, atom= 1703\n",
            "Step=  722, Dmax= 1.3e-02 nm, Epot= -1.68560e+06 Fmax= 1.04984e+04, atom= 1703\n",
            "Step=  723, Dmax= 1.6e-02 nm, Epot= -1.68554e+06 Fmax= 1.70520e+04, atom= 1703\rStep=  724, Dmax= 7.9e-03 nm, Epot= -1.68569e+06 Fmax= 4.71078e+03, atom= 1703\n",
            "Step=  725, Dmax= 9.5e-03 nm, Epot= -1.68572e+06 Fmax= 1.36802e+04, atom= 1703\n",
            "Step=  726, Dmax= 1.1e-02 nm, Epot= -1.68582e+06 Fmax= 8.03387e+03, atom= 1703\n",
            "Step=  727, Dmax= 1.4e-02 nm, Epot= -1.68578e+06 Fmax= 1.90525e+04, atom= 1703\rStep=  728, Dmax= 6.8e-03 nm, Epot= -1.68590e+06 Fmax= 4.26764e+03, atom= 1703\n",
            "Step=  729, Dmax= 8.2e-03 nm, Epot= -1.68595e+06 Fmax= 1.04867e+04, atom= 1703\n",
            "Step=  730, Dmax= 9.8e-03 nm, Epot= -1.68604e+06 Fmax= 7.54802e+03, atom= 1703\n",
            "Step=  731, Dmax= 1.2e-02 nm, Epot= -1.68605e+06 Fmax= 1.33755e+04, atom= 1703\n",
            "Step=  732, Dmax= 1.4e-02 nm, Epot= -1.68613e+06 Fmax= 1.27498e+04, atom= 1703\n",
            "Step=  733, Dmax= 1.7e-02 nm, Epot= -1.68609e+06 Fmax= 1.71070e+04, atom= 1703\rStep=  734, Dmax= 8.5e-03 nm, Epot= -1.68625e+06 Fmax= 3.87428e+03, atom= 1703\n",
            "Step=  735, Dmax= 1.0e-02 nm, Epot= -1.68628e+06 Fmax= 1.61351e+04, atom= 1704\n",
            "Step=  736, Dmax= 1.2e-02 nm, Epot= -1.68641e+06 Fmax= 7.61534e+03, atom= 1704\n",
            "Step=  737, Dmax= 1.5e-02 nm, Epot= -1.68632e+06 Fmax= 2.21753e+04, atom= 1703\rStep=  738, Dmax= 7.3e-03 nm, Epot= -1.68648e+06 Fmax= 5.81794e+03, atom= 1703\n",
            "Step=  739, Dmax= 8.8e-03 nm, Epot= -1.68652e+06 Fmax= 1.01114e+04, atom= 1703\n",
            "Step=  740, Dmax= 1.1e-02 nm, Epot= -1.68660e+06 Fmax= 9.49825e+03, atom= 1703\n",
            "Step=  741, Dmax= 1.3e-02 nm, Epot= -1.68661e+06 Fmax= 1.32166e+04, atom= 1703\n",
            "Step=  742, Dmax= 1.5e-02 nm, Epot= -1.68667e+06 Fmax= 1.52068e+04, atom= 1703\n",
            "Step=  743, Dmax= 1.8e-02 nm, Epot= -1.68664e+06 Fmax= 1.71709e+04, atom= 1703\rStep=  744, Dmax= 9.1e-03 nm, Epot= -1.68681e+06 Fmax= 2.98898e+03, atom= 1703\n",
            "Step=  745, Dmax= 1.1e-02 nm, Epot= -1.68686e+06 Fmax= 1.87603e+04, atom= 1704\n",
            "Step=  746, Dmax= 1.3e-02 nm, Epot= -1.68703e+06 Fmax= 7.27466e+03, atom= 1704\n",
            "Step=  747, Dmax= 1.6e-02 nm, Epot= -1.68688e+06 Fmax= 2.56438e+04, atom= 1703\rStep=  748, Dmax= 7.9e-03 nm, Epot= -1.68710e+06 Fmax= 7.49540e+03, atom= 1703\n",
            "Step=  749, Dmax= 9.5e-03 nm, Epot= -1.68713e+06 Fmax= 9.74778e+03, atom= 1703\n",
            "Step=  750, Dmax= 1.1e-02 nm, Epot= -1.68719e+06 Fmax= 1.16561e+04, atom= 1703\n",
            "Step=  751, Dmax= 1.4e-02 nm, Epot= -1.68721e+06 Fmax= 1.30346e+04, atom= 1703\n",
            "Step=  752, Dmax= 1.6e-02 nm, Epot= -1.68723e+06 Fmax= 1.79614e+04, atom= 1703\n",
            "Step=  753, Dmax= 2.0e-02 nm, Epot= -1.68725e+06 Fmax= 1.72141e+04, atom= 1703\n",
            "Step=  754, Dmax= 2.4e-02 nm, Epot= -1.68715e+06 Fmax= 2.76827e+04, atom= 1703\rStep=  755, Dmax= 1.2e-02 nm, Epot= -1.68749e+06 Fmax= 1.94985e+03, atom= 1699\n",
            "Step=  756, Dmax= 1.4e-02 nm, Epot= -1.68745e+06 Fmax= 2.44397e+04, atom= 1703\rStep=  757, Dmax= 7.1e-03 nm, Epot= -1.68760e+06 Fmax= 1.16379e+04, atom= 1703\n",
            "Step=  758, Dmax= 8.5e-03 nm, Epot= -1.68772e+06 Fmax= 4.06908e+03, atom= 1703\n",
            "Step=  759, Dmax= 1.0e-02 nm, Epot= -1.68775e+06 Fmax= 1.30510e+04, atom= 1704\n",
            "Step=  760, Dmax= 1.2e-02 nm, Epot= -1.68787e+06 Fmax= 9.06187e+03, atom= 1703\n",
            "Step=  761, Dmax= 1.5e-02 nm, Epot= -1.68782e+06 Fmax= 1.64941e+04, atom= 1703\rStep=  762, Dmax= 7.3e-03 nm, Epot= -1.68795e+06 Fmax= 4.94397e+03, atom= 1703\n",
            "Step=  763, Dmax= 8.8e-03 nm, Epot= -1.68798e+06 Fmax= 1.19315e+04, atom= 1703\n",
            "Step=  764, Dmax= 1.1e-02 nm, Epot= -1.68807e+06 Fmax= 8.00015e+03, atom= 1703\n",
            "Step=  765, Dmax= 1.3e-02 nm, Epot= -1.68805e+06 Fmax= 1.68090e+04, atom= 1703\rStep=  766, Dmax= 6.3e-03 nm, Epot= -1.68814e+06 Fmax= 3.35143e+03, atom= 1703\n",
            "Step=  767, Dmax= 7.6e-03 nm, Epot= -1.68820e+06 Fmax= 1.03288e+04, atom= 1703\n",
            "Step=  768, Dmax= 9.1e-03 nm, Epot= -1.68830e+06 Fmax= 6.33312e+03, atom= 1703\n",
            "Step=  769, Dmax= 1.1e-02 nm, Epot= -1.68830e+06 Fmax= 1.30042e+04, atom= 1703\n",
            "Step=  770, Dmax= 1.3e-02 nm, Epot= -1.68840e+06 Fmax= 1.11072e+04, atom= 1703\n",
            "Step=  771, Dmax= 1.6e-02 nm, Epot= -1.68835e+06 Fmax= 1.65385e+04, atom= 1703\rStep=  772, Dmax= 7.9e-03 nm, Epot= -1.68849e+06 Fmax= 4.15817e+03, atom= 1703\n",
            "Step=  773, Dmax= 9.4e-03 nm, Epot= -1.68853e+06 Fmax= 1.42615e+04, atom= 1703\n",
            "Step=  774, Dmax= 1.1e-02 nm, Epot= -1.68864e+06 Fmax= 7.54608e+03, atom= 1703\n",
            "Step=  775, Dmax= 1.4e-02 nm, Epot= -1.68858e+06 Fmax= 1.96789e+04, atom= 1703\rStep=  776, Dmax= 6.8e-03 nm, Epot= -1.68871e+06 Fmax= 4.82377e+03, atom= 1703\n",
            "Step=  777, Dmax= 8.2e-03 nm, Epot= -1.68875e+06 Fmax= 9.93430e+03, atom= 1703\n",
            "Step=  778, Dmax= 9.8e-03 nm, Epot= -1.68883e+06 Fmax= 8.15401e+03, atom= 1703\n",
            "Step=  779, Dmax= 1.2e-02 nm, Epot= -1.68883e+06 Fmax= 1.28505e+04, atom= 1703\n",
            "Step=  780, Dmax= 1.4e-02 nm, Epot= -1.68890e+06 Fmax= 1.33601e+04, atom= 1703\n",
            "Step=  781, Dmax= 1.7e-02 nm, Epot= -1.68887e+06 Fmax= 1.66103e+04, atom= 1703\rStep=  782, Dmax= 8.5e-03 nm, Epot= -1.68903e+06 Fmax= 3.33088e+03, atom= 1703\n",
            "Step=  783, Dmax= 1.0e-02 nm, Epot= -1.68906e+06 Fmax= 1.66928e+04, atom= 1704\n",
            "Step=  784, Dmax= 1.2e-02 nm, Epot= -1.68920e+06 Fmax= 7.16466e+03, atom= 1704\n",
            "Step=  785, Dmax= 1.5e-02 nm, Epot= -1.68910e+06 Fmax= 2.28242e+04, atom= 1703\rStep=  786, Dmax= 7.3e-03 nm, Epot= -1.68927e+06 Fmax= 6.37415e+03, atom= 1703\n",
            "Step=  787, Dmax= 8.8e-03 nm, Epot= -1.68930e+06 Fmax= 9.58359e+03, atom= 1703\n",
            "Step=  788, Dmax= 1.1e-02 nm, Epot= -1.68937e+06 Fmax= 1.01108e+04, atom= 1703\n",
            "Step=  789, Dmax= 1.3e-02 nm, Epot= -1.68938e+06 Fmax= 1.26981e+04, atom= 1703\n",
            "Step=  790, Dmax= 1.5e-02 nm, Epot= -1.68942e+06 Fmax= 1.58363e+04, atom= 1703\n",
            "Step=  791, Dmax= 1.8e-02 nm, Epot= -1.68941e+06 Fmax= 1.66828e+04, atom= 1703\rStep=  792, Dmax= 9.1e-03 nm, Epot= -1.68958e+06 Fmax= 2.44131e+03, atom= 1703\n",
            "Step=  793, Dmax= 1.1e-02 nm, Epot= -1.68964e+06 Fmax= 1.92569e+04, atom= 1704\n",
            "Step=  794, Dmax= 1.3e-02 nm, Epot= -1.68982e+06 Fmax= 6.91395e+03, atom= 1704\n",
            "Step=  795, Dmax= 1.6e-02 nm, Epot= -1.68964e+06 Fmax= 2.63241e+04, atom= 1703\rStep=  796, Dmax= 7.9e-03 nm, Epot= -1.68988e+06 Fmax= 8.04576e+03, atom= 1703\n",
            "Step=  797, Dmax= 9.4e-03 nm, Epot= -1.68991e+06 Fmax= 9.24114e+03, atom= 1703\n",
            "Step=  798, Dmax= 1.1e-02 nm, Epot= -1.68996e+06 Fmax= 1.22931e+04, atom= 1703\n",
            "Step=  799, Dmax= 1.4e-02 nm, Epot= -1.68999e+06 Fmax= 1.25188e+04, atom= 1703\n",
            "Step=  800, Dmax= 1.6e-02 nm, Epot= -1.68998e+06 Fmax= 1.86249e+04, atom= 1703\rStep=  801, Dmax= 8.2e-03 nm, Epot= -1.69012e+06 Fmax= 1.40398e+03, atom= 1703\n",
            "Step=  802, Dmax= 9.8e-03 nm, Epot= -1.69028e+06 Fmax= 1.69975e+04, atom= 1703\n",
            "Step=  803, Dmax= 1.2e-02 nm, Epot= -1.69051e+06 Fmax= 4.38891e+03, atom= 1703\n",
            "Step=  804, Dmax= 1.4e-02 nm, Epot= -1.69045e+06 Fmax= 1.82857e+04, atom= 1703\rStep=  805, Dmax= 7.0e-03 nm, Epot= -1.69056e+06 Fmax= 8.04981e+03, atom= 1704\n",
            "Step=  806, Dmax= 8.5e-03 nm, Epot= -1.69063e+06 Fmax= 7.85522e+03, atom= 1703\n",
            "Step=  807, Dmax= 1.0e-02 nm, Epot= -1.69065e+06 Fmax= 1.05769e+04, atom= 1703\n",
            "Step=  808, Dmax= 1.2e-02 nm, Epot= -1.69070e+06 Fmax= 1.23570e+04, atom= 1703\n",
            "Step=  809, Dmax= 1.5e-02 nm, Epot= -1.69070e+06 Fmax= 1.40208e+04, atom= 1703\n",
            "Step=  810, Dmax= 1.8e-02 nm, Epot= -1.69072e+06 Fmax= 1.91555e+04, atom= 1703\n",
            "Step=  811, Dmax= 2.1e-02 nm, Epot= -1.69072e+06 Fmax= 1.83537e+04, atom= 1703\rStep=  812, Dmax= 1.1e-02 nm, Epot= -1.69093e+06 Fmax= 2.31381e+03, atom= 1703\n",
            "Step=  813, Dmax= 1.3e-02 nm, Epot= -1.69097e+06 Fmax= 2.28822e+04, atom= 1704\n",
            "Step=  814, Dmax= 1.5e-02 nm, Epot= -1.69120e+06 Fmax= 7.89409e+03, atom= 1704\n",
            "Step=  815, Dmax= 1.8e-02 nm, Epot= -1.69090e+06 Fmax= 3.17631e+04, atom= 1703\rStep=  816, Dmax= 9.1e-03 nm, Epot= -1.69125e+06 Fmax= 9.74190e+03, atom= 1703\n",
            "Step=  817, Dmax= 1.1e-02 nm, Epot= -1.69129e+06 Fmax= 1.02222e+04, atom= 1703\n",
            "Step=  818, Dmax= 1.3e-02 nm, Epot= -1.69131e+06 Fmax= 1.49067e+04, atom= 1703\n",
            "Step=  819, Dmax= 1.6e-02 nm, Epot= -1.69134e+06 Fmax= 1.38037e+04, atom= 1703\n",
            "Step=  820, Dmax= 1.9e-02 nm, Epot= -1.69129e+06 Fmax= 2.24659e+04, atom= 1703\rStep=  821, Dmax= 9.4e-03 nm, Epot= -1.69150e+06 Fmax= 2.11233e+03, atom= 1703\n",
            "Step=  822, Dmax= 1.1e-02 nm, Epot= -1.69153e+06 Fmax= 1.86113e+04, atom= 1703\n",
            "Step=  823, Dmax= 1.4e-02 nm, Epot= -1.69180e+06 Fmax= 5.75643e+03, atom= 1703\n",
            "Step=  824, Dmax= 1.6e-02 nm, Epot= -1.69164e+06 Fmax= 2.06875e+04, atom= 1703\rStep=  825, Dmax= 8.1e-03 nm, Epot= -1.69184e+06 Fmax= 8.84342e+03, atom= 1703\n",
            "Step=  826, Dmax= 9.8e-03 nm, Epot= -1.69189e+06 Fmax= 9.54429e+03, atom= 1703\n",
            "Step=  827, Dmax= 1.2e-02 nm, Epot= -1.69192e+06 Fmax= 1.17074e+04, atom= 1703\n",
            "Step=  828, Dmax= 1.4e-02 nm, Epot= -1.69195e+06 Fmax= 1.48558e+04, atom= 1703\n",
            "Step=  829, Dmax= 1.7e-02 nm, Epot= -1.69195e+06 Fmax= 1.55125e+04, atom= 1703\n",
            "Step=  830, Dmax= 2.0e-02 nm, Epot= -1.69192e+06 Fmax= 2.29404e+04, atom= 1703\rStep=  831, Dmax= 1.0e-02 nm, Epot= -1.69215e+06 Fmax= 1.40695e+03, atom= 1699\n",
            "Step=  832, Dmax= 1.2e-02 nm, Epot= -1.69227e+06 Fmax= 2.03650e+04, atom= 1703\n",
            "Step=  833, Dmax= 1.5e-02 nm, Epot= -1.69258e+06 Fmax= 7.47929e+03, atom= 1703\n",
            "Step=  834, Dmax= 1.7e-02 nm, Epot= -1.69243e+06 Fmax= 2.02038e+04, atom= 1703\rStep=  835, Dmax= 8.7e-03 nm, Epot= -1.69263e+06 Fmax= 8.31458e+03, atom= 1704\n",
            "Step=  836, Dmax= 1.0e-02 nm, Epot= -1.69266e+06 Fmax= 1.19745e+04, atom= 1703\n",
            "Step=  837, Dmax= 1.3e-02 nm, Epot= -1.69270e+06 Fmax= 1.12569e+04, atom= 1703\n",
            "Step=  838, Dmax= 1.5e-02 nm, Epot= -1.69268e+06 Fmax= 1.79520e+04, atom= 1703\rStep=  839, Dmax= 7.6e-03 nm, Epot= -1.69281e+06 Fmax= 1.90893e+03, atom= 1703\n",
            "Step=  840, Dmax= 9.1e-03 nm, Epot= -1.69290e+06 Fmax= 1.44821e+04, atom= 1703\n",
            "Step=  841, Dmax= 1.1e-02 nm, Epot= -1.69306e+06 Fmax= 5.15269e+03, atom= 1703\n",
            "Step=  842, Dmax= 1.3e-02 nm, Epot= -1.69300e+06 Fmax= 1.69434e+04, atom= 1703\rStep=  843, Dmax= 6.5e-03 nm, Epot= -1.69311e+06 Fmax= 6.81990e+03, atom= 1703\n",
            "Step=  844, Dmax= 7.8e-03 nm, Epot= -1.69316e+06 Fmax= 7.99120e+03, atom= 1703\n",
            "Step=  845, Dmax= 9.4e-03 nm, Epot= -1.69319e+06 Fmax= 9.28483e+03, atom= 1703\n",
            "Step=  846, Dmax= 1.1e-02 nm, Epot= -1.69323e+06 Fmax= 1.21352e+04, atom= 1703\n",
            "Step=  847, Dmax= 1.4e-02 nm, Epot= -1.69326e+06 Fmax= 1.25975e+04, atom= 1703\n",
            "Step=  848, Dmax= 1.6e-02 nm, Epot= -1.69326e+06 Fmax= 1.84107e+04, atom= 1703\rStep=  849, Dmax= 8.1e-03 nm, Epot= -1.69340e+06 Fmax= 1.27717e+03, atom= 1703\n",
            "Step=  850, Dmax= 9.7e-03 nm, Epot= -1.69355e+06 Fmax= 1.73140e+04, atom= 1703\n",
            "Step=  851, Dmax= 1.2e-02 nm, Epot= -1.69379e+06 Fmax= 4.11303e+03, atom= 1703\n",
            "Step=  852, Dmax= 1.4e-02 nm, Epot= -1.69372e+06 Fmax= 1.81807e+04, atom= 1703\rStep=  853, Dmax= 7.0e-03 nm, Epot= -1.69384e+06 Fmax= 8.15940e+03, atom= 1704\n",
            "Step=  854, Dmax= 8.4e-03 nm, Epot= -1.69389e+06 Fmax= 7.66720e+03, atom= 1703\n",
            "Step=  855, Dmax= 1.0e-02 nm, Epot= -1.69392e+06 Fmax= 1.06985e+04, atom= 1703\n",
            "Step=  856, Dmax= 1.2e-02 nm, Epot= -1.69397e+06 Fmax= 1.21323e+04, atom= 1703\n",
            "Step=  857, Dmax= 1.5e-02 nm, Epot= -1.69396e+06 Fmax= 1.41382e+04, atom= 1703\rStep=  858, Dmax= 7.3e-03 nm, Epot= -1.69407e+06 Fmax= 2.29046e+03, atom= 1703\n",
            "Step=  859, Dmax= 8.7e-03 nm, Epot= -1.69414e+06 Fmax= 1.48979e+04, atom= 1704\n",
            "Step=  860, Dmax= 1.0e-02 nm, Epot= -1.69426e+06 Fmax= 5.71113e+03, atom= 1704\n",
            "Step=  861, Dmax= 1.3e-02 nm, Epot= -1.69419e+06 Fmax= 2.01430e+04, atom= 1703\rStep=  862, Dmax= 6.3e-03 nm, Epot= -1.69431e+06 Fmax= 6.15071e+03, atom= 1703\n",
            "Step=  863, Dmax= 7.5e-03 nm, Epot= -1.69435e+06 Fmax= 7.75567e+03, atom= 1703\n",
            "Step=  864, Dmax= 9.1e-03 nm, Epot= -1.69440e+06 Fmax= 9.38584e+03, atom= 1703\n",
            "Step=  865, Dmax= 1.1e-02 nm, Epot= -1.69443e+06 Fmax= 1.05541e+04, atom= 1703\n",
            "Step=  866, Dmax= 1.3e-02 nm, Epot= -1.69445e+06 Fmax= 1.42438e+04, atom= 1703\n",
            "Step=  867, Dmax= 1.6e-02 nm, Epot= -1.69448e+06 Fmax= 1.42375e+04, atom= 1703\n",
            "Step=  868, Dmax= 1.9e-02 nm, Epot= -1.69444e+06 Fmax= 2.16627e+04, atom= 1703\rStep=  869, Dmax= 9.4e-03 nm, Epot= -1.69463e+06 Fmax= 1.54423e+03, atom= 1703\n",
            "Step=  870, Dmax= 1.1e-02 nm, Epot= -1.69469e+06 Fmax= 2.00196e+04, atom= 1703\n",
            "Step=  871, Dmax= 1.4e-02 nm, Epot= -1.69500e+06 Fmax= 4.67044e+03, atom= 1703\n",
            "Step=  872, Dmax= 1.6e-02 nm, Epot= -1.69487e+06 Fmax= 2.05405e+04, atom= 1703\rStep=  873, Dmax= 8.1e-03 nm, Epot= -1.69504e+06 Fmax= 9.36067e+03, atom= 1704\n",
            "Step=  874, Dmax= 9.7e-03 nm, Epot= -1.69510e+06 Fmax= 8.90958e+03, atom= 1703\n",
            "Step=  875, Dmax= 1.2e-02 nm, Epot= -1.69510e+06 Fmax= 1.21894e+04, atom= 1703\n",
            "Step=  876, Dmax= 1.4e-02 nm, Epot= -1.69515e+06 Fmax= 1.41547e+04, atom= 1703\n",
            "Step=  877, Dmax= 1.7e-02 nm, Epot= -1.69513e+06 Fmax= 1.59664e+04, atom= 1703\rStep=  878, Dmax= 8.4e-03 nm, Epot= -1.69528e+06 Fmax= 2.61735e+03, atom= 1703\n",
            "Step=  879, Dmax= 1.0e-02 nm, Epot= -1.69531e+06 Fmax= 1.73684e+04, atom= 1704\n",
            "Step=  880, Dmax= 1.2e-02 nm, Epot= -1.69546e+06 Fmax= 6.60042e+03, atom= 1703\n",
            "Step=  881, Dmax= 1.5e-02 nm, Epot= -1.69532e+06 Fmax= 2.36766e+04, atom= 1703\rStep=  882, Dmax= 7.3e-03 nm, Epot= -1.69551e+06 Fmax= 7.10273e+03, atom= 1703\n",
            "Step=  883, Dmax= 8.7e-03 nm, Epot= -1.69554e+06 Fmax= 8.89290e+03, atom= 1703\n",
            "Step=  884, Dmax= 1.0e-02 nm, Epot= -1.69559e+06 Fmax= 1.09061e+04, atom= 1703\n",
            "Step=  885, Dmax= 1.3e-02 nm, Epot= -1.69561e+06 Fmax= 1.20140e+04, atom= 1703\n",
            "Step=  886, Dmax= 1.5e-02 nm, Epot= -1.69562e+06 Fmax= 1.66376e+04, atom= 1703\n",
            "Step=  887, Dmax= 1.8e-02 nm, Epot= -1.69563e+06 Fmax= 1.60438e+04, atom= 1703\n",
            "Step=  888, Dmax= 2.2e-02 nm, Epot= -1.69555e+06 Fmax= 2.54431e+04, atom= 1703\rStep=  889, Dmax= 1.1e-02 nm, Epot= -1.69584e+06 Fmax= 1.81691e+03, atom= 1704\n",
            "Step=  890, Dmax= 1.3e-02 nm, Epot= -1.69576e+06 Fmax= 2.32484e+04, atom= 1703\rStep=  891, Dmax= 6.5e-03 nm, Epot= -1.69592e+06 Fmax= 1.11413e+04, atom= 1703\n",
            "Step=  892, Dmax= 7.8e-03 nm, Epot= -1.69603e+06 Fmax= 3.25434e+03, atom= 1703\n",
            "Step=  893, Dmax= 9.4e-03 nm, Epot= -1.69606e+06 Fmax= 1.25234e+04, atom= 1704\n",
            "Step=  894, Dmax= 1.1e-02 nm, Epot= -1.69617e+06 Fmax= 7.79594e+03, atom= 1703\n",
            "Step=  895, Dmax= 1.3e-02 nm, Epot= -1.69611e+06 Fmax= 1.58576e+04, atom= 1703\rStep=  896, Dmax= 6.7e-03 nm, Epot= -1.69623e+06 Fmax= 5.06453e+03, atom= 1703\n",
            "Step=  897, Dmax= 8.1e-03 nm, Epot= -1.69626e+06 Fmax= 1.03837e+04, atom= 1703\n",
            "Step=  898, Dmax= 9.7e-03 nm, Epot= -1.69632e+06 Fmax= 7.89143e+03, atom= 1703\n",
            "Step=  899, Dmax= 1.2e-02 nm, Epot= -1.69631e+06 Fmax= 1.47529e+04, atom= 1703\rStep=  900, Dmax= 5.8e-03 nm, Epot= -1.69638e+06 Fmax= 2.55340e+03, atom= 1703\n",
            "Step=  901, Dmax= 7.0e-03 nm, Epot= -1.69645e+06 Fmax= 1.01255e+04, atom= 1703\n",
            "Step=  902, Dmax= 8.4e-03 nm, Epot= -1.69654e+06 Fmax= 5.21916e+03, atom= 1703\n",
            "Step=  903, Dmax= 1.0e-02 nm, Epot= -1.69654e+06 Fmax= 1.25924e+04, atom= 1703\rStep=  904, Dmax= 5.0e-03 nm, Epot= -1.69658e+06 Fmax= 4.26572e+03, atom= 1703\n",
            "Step=  905, Dmax= 6.0e-03 nm, Epot= -1.69663e+06 Fmax= 7.25910e+03, atom= 1703\n",
            "Step=  906, Dmax= 7.3e-03 nm, Epot= -1.69668e+06 Fmax= 6.33318e+03, atom= 1703\n",
            "Step=  907, Dmax= 8.7e-03 nm, Epot= -1.69670e+06 Fmax= 1.03900e+04, atom= 1703\n",
            "Step=  908, Dmax= 1.0e-02 nm, Epot= -1.69675e+06 Fmax= 9.09758e+03, atom= 1703\n",
            "Step=  909, Dmax= 1.3e-02 nm, Epot= -1.69675e+06 Fmax= 1.51047e+04, atom= 1703\rStep=  910, Dmax= 6.3e-03 nm, Epot= -1.69683e+06 Fmax= 2.00641e+03, atom= 1703\n",
            "Step=  911, Dmax= 7.5e-03 nm, Epot= -1.69692e+06 Fmax= 1.16648e+04, atom= 1703\n",
            "Step=  912, Dmax= 9.0e-03 nm, Epot= -1.69702e+06 Fmax= 4.74527e+03, atom= 1703\n",
            "Step=  913, Dmax= 1.1e-02 nm, Epot= -1.69700e+06 Fmax= 1.40965e+04, atom= 1703\rStep=  914, Dmax= 5.4e-03 nm, Epot= -1.69707e+06 Fmax= 5.33141e+03, atom= 1703\n",
            "Step=  915, Dmax= 6.5e-03 nm, Epot= -1.69711e+06 Fmax= 6.99678e+03, atom= 1703\n",
            "Step=  916, Dmax= 7.8e-03 nm, Epot= -1.69715e+06 Fmax= 7.48179e+03, atom= 1703\n",
            "Step=  917, Dmax= 9.4e-03 nm, Epot= -1.69719e+06 Fmax= 1.03588e+04, atom= 1703\n",
            "Step=  918, Dmax= 1.1e-02 nm, Epot= -1.69722e+06 Fmax= 1.03881e+04, atom= 1703\n",
            "Step=  919, Dmax= 1.3e-02 nm, Epot= -1.69722e+06 Fmax= 1.54278e+04, atom= 1703\n",
            "Step=  920, Dmax= 1.6e-02 nm, Epot= -1.69726e+06 Fmax= 1.41923e+04, atom= 1703\n",
            "Step=  921, Dmax= 1.9e-02 nm, Epot= -1.69719e+06 Fmax= 2.31864e+04, atom= 1703\rStep=  922, Dmax= 9.7e-03 nm, Epot= -1.69742e+06 Fmax= 2.15330e+03, atom= 1703\n",
            "Step=  923, Dmax= 1.2e-02 nm, Epot= -1.69739e+06 Fmax= 1.93398e+04, atom= 1703\rStep=  924, Dmax= 5.8e-03 nm, Epot= -1.69749e+06 Fmax= 9.10988e+03, atom= 1703\n",
            "Step=  925, Dmax= 7.0e-03 nm, Epot= -1.69757e+06 Fmax= 3.70995e+03, atom= 1703\n",
            "Step=  926, Dmax= 8.4e-03 nm, Epot= -1.69759e+06 Fmax= 1.10336e+04, atom= 1703\n",
            "Step=  927, Dmax= 1.0e-02 nm, Epot= -1.69768e+06 Fmax= 7.39229e+03, atom= 1703\n",
            "Step=  928, Dmax= 1.2e-02 nm, Epot= -1.69765e+06 Fmax= 1.39895e+04, atom= 1703\rStep=  929, Dmax= 6.0e-03 nm, Epot= -1.69774e+06 Fmax= 4.13959e+03, atom= 1703\n",
            "Step=  930, Dmax= 7.2e-03 nm, Epot= -1.69777e+06 Fmax= 9.77894e+03, atom= 1703\n",
            "Step=  931, Dmax= 8.7e-03 nm, Epot= -1.69783e+06 Fmax= 6.68657e+03, atom= 1703\n",
            "Step=  932, Dmax= 1.0e-02 nm, Epot= -1.69783e+06 Fmax= 1.36537e+04, atom= 1703\rStep=  933, Dmax= 5.2e-03 nm, Epot= -1.69789e+06 Fmax= 2.77725e+03, atom= 1703\n",
            "Step=  934, Dmax= 6.3e-03 nm, Epot= -1.69795e+06 Fmax= 8.62328e+03, atom= 1703\n",
            "Step=  935, Dmax= 7.5e-03 nm, Epot= -1.69801e+06 Fmax= 5.20864e+03, atom= 1703\n",
            "Step=  936, Dmax= 9.0e-03 nm, Epot= -1.69803e+06 Fmax= 1.09514e+04, atom= 1703\n",
            "Step=  937, Dmax= 1.1e-02 nm, Epot= -1.69810e+06 Fmax= 9.04763e+03, atom= 1703\n",
            "Step=  938, Dmax= 1.3e-02 nm, Epot= -1.69807e+06 Fmax= 1.40885e+04, atom= 1703\rStep=  939, Dmax= 6.5e-03 nm, Epot= -1.69817e+06 Fmax= 3.50929e+03, atom= 1703\n",
            "Step=  940, Dmax= 7.8e-03 nm, Epot= -1.69820e+06 Fmax= 1.16066e+04, atom= 1703\n",
            "Step=  941, Dmax= 9.3e-03 nm, Epot= -1.69828e+06 Fmax= 6.33352e+03, atom= 1703\n",
            "Step=  942, Dmax= 1.1e-02 nm, Epot= -1.69825e+06 Fmax= 1.58895e+04, atom= 1703\rStep=  943, Dmax= 5.6e-03 nm, Epot= -1.69833e+06 Fmax= 3.94758e+03, atom= 1703\n",
            "Step=  944, Dmax= 6.7e-03 nm, Epot= -1.69837e+06 Fmax= 8.34283e+03, atom= 1703\n",
            "Step=  945, Dmax= 8.1e-03 nm, Epot= -1.69843e+06 Fmax= 6.64455e+03, atom= 1703\n",
            "Step=  946, Dmax= 9.7e-03 nm, Epot= -1.69844e+06 Fmax= 1.08721e+04, atom= 1703\n",
            "Step=  947, Dmax= 1.2e-02 nm, Epot= -1.69850e+06 Fmax= 1.08206e+04, atom= 1703\n",
            "Step=  948, Dmax= 1.4e-02 nm, Epot= -1.69848e+06 Fmax= 1.42178e+04, atom= 1703\rStep=  949, Dmax= 7.0e-03 nm, Epot= -1.69859e+06 Fmax= 2.86141e+03, atom= 1703\n",
            "Step=  950, Dmax= 8.4e-03 nm, Epot= -1.69863e+06 Fmax= 1.35119e+04, atom= 1703\n",
            "Step=  951, Dmax= 1.0e-02 nm, Epot= -1.69873e+06 Fmax= 6.03695e+03, atom= 1703\n",
            "Step=  952, Dmax= 1.2e-02 nm, Epot= -1.69866e+06 Fmax= 1.83072e+04, atom= 1703\rStep=  953, Dmax= 6.0e-03 nm, Epot= -1.69877e+06 Fmax= 5.16155e+03, atom= 1703\n",
            "Step=  954, Dmax= 7.2e-03 nm, Epot= -1.69881e+06 Fmax= 8.10678e+03, atom= 1703\n",
            "Step=  955, Dmax= 8.7e-03 nm, Epot= -1.69886e+06 Fmax= 8.16042e+03, atom= 1703\n",
            "Step=  956, Dmax= 1.0e-02 nm, Epot= -1.69887e+06 Fmax= 1.08141e+04, atom= 1703\n",
            "Step=  957, Dmax= 1.2e-02 nm, Epot= -1.69891e+06 Fmax= 1.27331e+04, atom= 1703\n",
            "Step=  958, Dmax= 1.5e-02 nm, Epot= -1.69890e+06 Fmax= 1.43707e+04, atom= 1703\rStep=  959, Dmax= 7.5e-03 nm, Epot= -1.69902e+06 Fmax= 2.18681e+03, atom= 1703\n",
            "Step=  960, Dmax= 9.0e-03 nm, Epot= -1.69908e+06 Fmax= 1.55201e+04, atom= 1704\n",
            "Step=  961, Dmax= 1.1e-02 nm, Epot= -1.69920e+06 Fmax= 5.79294e+03, atom= 1703\n",
            "Step=  962, Dmax= 1.3e-02 nm, Epot= -1.69910e+06 Fmax= 2.10356e+04, atom= 1703\rStep=  963, Dmax= 6.5e-03 nm, Epot= -1.69925e+06 Fmax= 6.49103e+03, atom= 1703\n",
            "Step=  964, Dmax= 7.8e-03 nm, Epot= -1.69928e+06 Fmax= 7.85449e+03, atom= 1703\n",
            "Step=  965, Dmax= 9.3e-03 nm, Epot= -1.69932e+06 Fmax= 9.85301e+03, atom= 1703\n",
            "Step=  966, Dmax= 1.1e-02 nm, Epot= -1.69934e+06 Fmax= 1.07251e+04, atom= 1703\n",
            "Step=  967, Dmax= 1.3e-02 nm, Epot= -1.69935e+06 Fmax= 1.48813e+04, atom= 1703\n",
            "Step=  968, Dmax= 1.6e-02 nm, Epot= -1.69936e+06 Fmax= 1.44993e+04, atom= 1703\n",
            "Step=  969, Dmax= 1.9e-02 nm, Epot= -1.69931e+06 Fmax= 2.25672e+04, atom= 1703\rStep=  970, Dmax= 9.7e-03 nm, Epot= -1.69953e+06 Fmax= 1.73188e+03, atom= 1703\n",
            "Step=  971, Dmax= 1.2e-02 nm, Epot= -1.69952e+06 Fmax= 2.02722e+04, atom= 1703\rStep=  972, Dmax= 5.8e-03 nm, Epot= -1.69961e+06 Fmax= 9.70329e+03, atom= 1703\n",
            "Step=  973, Dmax= 7.0e-03 nm, Epot= -1.69970e+06 Fmax= 3.14195e+03, atom= 1703\n",
            "Step=  974, Dmax= 8.4e-03 nm, Epot= -1.69973e+06 Fmax= 1.12642e+04, atom= 1703\n",
            "Step=  975, Dmax= 1.0e-02 nm, Epot= -1.69983e+06 Fmax= 7.00756e+03, atom= 1703\n",
            "Step=  976, Dmax= 1.2e-02 nm, Epot= -1.69978e+06 Fmax= 1.42779e+04, atom= 1703\rStep=  977, Dmax= 6.0e-03 nm, Epot= -1.69988e+06 Fmax= 4.46567e+03, atom= 1703\n",
            "Step=  978, Dmax= 7.2e-03 nm, Epot= -1.69991e+06 Fmax= 9.33960e+03, atom= 1703\n",
            "Step=  979, Dmax= 8.7e-03 nm, Epot= -1.69996e+06 Fmax= 7.00490e+03, atom= 1703\n",
            "Step=  980, Dmax= 1.0e-02 nm, Epot= -1.69996e+06 Fmax= 1.31710e+04, atom= 1703\rStep=  981, Dmax= 5.2e-03 nm, Epot= -1.70002e+06 Fmax= 2.38718e+03, atom= 1703\n",
            "Step=  982, Dmax= 6.2e-03 nm, Epot= -1.70008e+06 Fmax= 8.98199e+03, atom= 1703\n",
            "Step=  983, Dmax= 7.5e-03 nm, Epot= -1.70015e+06 Fmax= 4.76836e+03, atom= 1703\n",
            "Step=  984, Dmax= 9.0e-03 nm, Epot= -1.70016e+06 Fmax= 1.12690e+04, atom= 1703\n",
            "Step=  985, Dmax= 1.1e-02 nm, Epot= -1.70024e+06 Fmax= 8.59151e+03, atom= 1703\n",
            "Step=  986, Dmax= 1.3e-02 nm, Epot= -1.70020e+06 Fmax= 1.43888e+04, atom= 1703\rStep=  987, Dmax= 6.5e-03 nm, Epot= -1.70030e+06 Fmax= 3.87183e+03, atom= 1703\n",
            "Step=  988, Dmax= 7.8e-03 nm, Epot= -1.70033e+06 Fmax= 1.11503e+04, atom= 1703\n",
            "Step=  989, Dmax= 9.3e-03 nm, Epot= -1.70039e+06 Fmax= 6.65178e+03, atom= 1703\n",
            "Step=  990, Dmax= 1.1e-02 nm, Epot= -1.70037e+06 Fmax= 1.53745e+04, atom= 1703\rStep=  991, Dmax= 5.6e-03 nm, Epot= -1.70045e+06 Fmax= 3.54245e+03, atom= 1703\n",
            "Step=  992, Dmax= 6.7e-03 nm, Epot= -1.70048e+06 Fmax= 8.68979e+03, atom= 1703\n",
            "Step=  993, Dmax= 8.0e-03 nm, Epot= -1.70055e+06 Fmax= 6.19241e+03, atom= 1703\n",
            "Step=  994, Dmax= 9.7e-03 nm, Epot= -1.70056e+06 Fmax= 1.11976e+04, atom= 1703\n",
            "Step=  995, Dmax= 1.2e-02 nm, Epot= -1.70062e+06 Fmax= 1.03368e+04, atom= 1703\n",
            "Step=  996, Dmax= 1.4e-02 nm, Epot= -1.70059e+06 Fmax= 1.45220e+04, atom= 1703\rStep=  997, Dmax= 7.0e-03 nm, Epot= -1.70070e+06 Fmax= 3.23694e+03, atom= 1703\n",
            "Step=  998, Dmax= 8.3e-03 nm, Epot= -1.70072e+06 Fmax= 1.30496e+04, atom= 1703\n",
            "Step=  999, Dmax= 1.0e-02 nm, Epot= -1.70081e+06 Fmax= 6.34078e+03, atom= 1703\n",
            "Step= 1000, Dmax= 1.2e-02 nm, Epot= -1.70076e+06 Fmax= 1.77549e+04, atom= 1703\rStep= 1001, Dmax= 6.0e-03 nm, Epot= -1.70086e+06 Fmax= 4.74543e+03, atom= 1703\n",
            "Step= 1002, Dmax= 7.2e-03 nm, Epot= -1.70089e+06 Fmax= 8.44702e+03, atom= 1703\n",
            "Step= 1003, Dmax= 8.6e-03 nm, Epot= -1.70094e+06 Fmax= 7.69093e+03, atom= 1703\n",
            "Step= 1004, Dmax= 1.0e-02 nm, Epot= -1.70095e+06 Fmax= 1.11424e+04, atom= 1703\n",
            "Step= 1005, Dmax= 1.2e-02 nm, Epot= -1.70099e+06 Fmax= 1.22211e+04, atom= 1703\n",
            "Step= 1006, Dmax= 1.5e-02 nm, Epot= -1.70098e+06 Fmax= 1.46768e+04, atom= 1703\rStep= 1007, Dmax= 7.5e-03 nm, Epot= -1.70109e+06 Fmax= 2.57384e+03, atom= 1703\n",
            "Step= 1008, Dmax= 9.0e-03 nm, Epot= -1.70112e+06 Fmax= 1.50539e+04, atom= 1704\n",
            "Step= 1009, Dmax= 1.1e-02 nm, Epot= -1.70124e+06 Fmax= 6.08302e+03, atom= 1703\n",
            "Step= 1010, Dmax= 1.3e-02 nm, Epot= -1.70115e+06 Fmax= 2.03904e+04, atom= 1703\rStep= 1011, Dmax= 6.5e-03 nm, Epot= -1.70129e+06 Fmax= 6.03095e+03, atom= 1703\n",
            "Step= 1012, Dmax= 7.7e-03 nm, Epot= -1.70132e+06 Fmax= 8.21885e+03, atom= 1703\n",
            "Step= 1013, Dmax= 9.3e-03 nm, Epot= -1.70136e+06 Fmax= 9.32115e+03, atom= 1703\n",
            "Step= 1014, Dmax= 1.1e-02 nm, Epot= -1.70137e+06 Fmax= 1.10854e+04, atom= 1703\n",
            "Step= 1015, Dmax= 1.3e-02 nm, Epot= -1.70139e+06 Fmax= 1.42964e+04, atom= 1703\n",
            "Step= 1016, Dmax= 1.6e-02 nm, Epot= -1.70139e+06 Fmax= 1.48340e+04, atom= 1703\rStep= 1017, Dmax= 8.0e-03 nm, Epot= -1.70152e+06 Fmax= 1.85391e+03, atom= 1703\n",
            "Step= 1018, Dmax= 9.6e-03 nm, Epot= -1.70158e+06 Fmax= 1.71545e+04, atom= 1704\n",
            "Step= 1019, Dmax= 1.2e-02 nm, Epot= -1.70173e+06 Fmax= 5.92432e+03, atom= 1704\n",
            "Step= 1020, Dmax= 1.4e-02 nm, Epot= -1.70158e+06 Fmax= 2.33996e+04, atom= 1703\rStep= 1021, Dmax= 6.9e-03 nm, Epot= -1.70177e+06 Fmax= 7.45803e+03, atom= 1703\n",
            "Step= 1022, Dmax= 8.3e-03 nm, Epot= -1.70180e+06 Fmax= 7.95691e+03, atom= 1703\n",
            "Step= 1023, Dmax= 1.0e-02 nm, Epot= -1.70182e+06 Fmax= 1.11861e+04, atom= 1703\n",
            "Step= 1024, Dmax= 1.2e-02 nm, Epot= -1.70185e+06 Fmax= 1.09716e+04, atom= 1703\n",
            "Step= 1025, Dmax= 1.4e-02 nm, Epot= -1.70184e+06 Fmax= 1.66734e+04, atom= 1703\rStep= 1026, Dmax= 7.2e-03 nm, Epot= -1.70195e+06 Fmax= 1.56026e+03, atom= 1703\n",
            "Step= 1027, Dmax= 8.6e-03 nm, Epot= -1.70203e+06 Fmax= 1.44012e+04, atom= 1703\n",
            "Step= 1028, Dmax= 1.0e-02 nm, Epot= -1.70219e+06 Fmax= 4.42138e+03, atom= 1703\n",
            "Step= 1029, Dmax= 1.2e-02 nm, Epot= -1.70212e+06 Fmax= 1.64983e+04, atom= 1703\rStep= 1030, Dmax= 6.2e-03 nm, Epot= -1.70223e+06 Fmax= 6.88665e+03, atom= 1703\n",
            "Step= 1031, Dmax= 7.5e-03 nm, Epot= -1.70227e+06 Fmax= 7.21158e+03, atom= 1703\n",
            "Step= 1032, Dmax= 9.0e-03 nm, Epot= -1.70229e+06 Fmax= 9.22766e+03, atom= 1703\n",
            "Step= 1033, Dmax= 1.1e-02 nm, Epot= -1.70232e+06 Fmax= 1.11147e+04, atom= 1703\n",
            "Step= 1034, Dmax= 1.3e-02 nm, Epot= -1.70233e+06 Fmax= 1.24263e+04, atom= 1703\n",
            "Step= 1035, Dmax= 1.5e-02 nm, Epot= -1.70233e+06 Fmax= 1.69977e+04, atom= 1703\n",
            "Step= 1036, Dmax= 1.9e-02 nm, Epot= -1.70233e+06 Fmax= 1.65363e+04, atom= 1703\rStep= 1037, Dmax= 9.3e-03 nm, Epot= -1.70250e+06 Fmax= 1.89344e+03, atom= 1703\n",
            "Step= 1038, Dmax= 1.1e-02 nm, Epot= -1.70254e+06 Fmax= 2.01592e+04, atom= 1704\n",
            "Step= 1039, Dmax= 1.3e-02 nm, Epot= -1.70272e+06 Fmax= 6.85515e+03, atom= 1704\n",
            "Step= 1040, Dmax= 1.6e-02 nm, Epot= -1.70248e+06 Fmax= 2.78623e+04, atom= 1703\rStep= 1041, Dmax= 8.0e-03 nm, Epot= -1.70275e+06 Fmax= 8.81088e+03, atom= 1703\n",
            "Step= 1042, Dmax= 9.6e-03 nm, Epot= -1.70279e+06 Fmax= 8.96388e+03, atom= 1703\n",
            "Step= 1043, Dmax= 1.2e-02 nm, Epot= -1.70279e+06 Fmax= 1.32947e+04, atom= 1703\n",
            "Step= 1044, Dmax= 1.4e-02 nm, Epot= -1.70282e+06 Fmax= 1.22867e+04, atom= 1703\n",
            "Step= 1045, Dmax= 1.7e-02 nm, Epot= -1.70278e+06 Fmax= 1.98161e+04, atom= 1703\rStep= 1046, Dmax= 8.3e-03 nm, Epot= -1.70295e+06 Fmax= 2.03520e+03, atom= 1703\n",
            "Step= 1047, Dmax= 1.0e-02 nm, Epot= -1.70296e+06 Fmax= 1.62160e+04, atom= 1703\n",
            "Step= 1048, Dmax= 1.2e-02 nm, Epot= -1.70315e+06 Fmax= 5.37902e+03, atom= 1703\n",
            "Step= 1049, Dmax= 1.4e-02 nm, Epot= -1.70302e+06 Fmax= 1.86067e+04, atom= 1703\rStep= 1050, Dmax= 7.2e-03 nm, Epot= -1.70318e+06 Fmax= 7.71205e+03, atom= 1703\n",
            "Step= 1051, Dmax= 8.6e-03 nm, Epot= -1.70322e+06 Fmax= 8.57510e+03, atom= 1703\n",
            "Step= 1052, Dmax= 1.0e-02 nm, Epot= -1.70323e+06 Fmax= 1.03671e+04, atom= 1703\n",
            "Step= 1053, Dmax= 1.2e-02 nm, Epot= -1.70325e+06 Fmax= 1.31701e+04, atom= 1703\n",
            "Step= 1054, Dmax= 1.5e-02 nm, Epot= -1.70326e+06 Fmax= 1.39179e+04, atom= 1703\n",
            "Step= 1055, Dmax= 1.8e-02 nm, Epot= -1.70323e+06 Fmax= 2.01464e+04, atom= 1703\rStep= 1056, Dmax= 8.9e-03 nm, Epot= -1.70341e+06 Fmax= 1.17156e+03, atom= 1699\n",
            "Step= 1057, Dmax= 1.1e-02 nm, Epot= -1.70347e+06 Fmax= 2.00055e+04, atom= 1703\n",
            "Step= 1058, Dmax= 1.3e-02 nm, Epot= -1.70377e+06 Fmax= 3.92926e+03, atom= 1703\n",
            "Step= 1059, Dmax= 1.5e-02 nm, Epot= -1.70365e+06 Fmax= 1.90971e+04, atom= 1703\rStep= 1060, Dmax= 7.7e-03 nm, Epot= -1.70380e+06 Fmax= 9.05784e+03, atom= 1704\n",
            "Step= 1061, Dmax= 9.3e-03 nm, Epot= -1.70385e+06 Fmax= 8.21599e+03, atom= 1703\n",
            "Step= 1062, Dmax= 1.1e-02 nm, Epot= -1.70384e+06 Fmax= 1.19311e+04, atom= 1703\rStep= 1063, Dmax= 5.6e-03 nm, Epot= -1.70390e+06 Fmax= 2.60820e+03, atom= 1703\n",
            "Step= 1064, Dmax= 6.7e-03 nm, Epot= -1.70395e+06 Fmax= 1.03527e+04, atom= 1703\n",
            "Step= 1065, Dmax= 8.0e-03 nm, Epot= -1.70402e+06 Fmax= 5.06919e+03, atom= 1703\n",
            "Step= 1066, Dmax= 9.6e-03 nm, Epot= -1.70400e+06 Fmax= 1.40250e+04, atom= 1703\rStep= 1067, Dmax= 4.8e-03 nm, Epot= -1.70406e+06 Fmax= 3.86519e+03, atom= 1703\n",
            "Step= 1068, Dmax= 5.8e-03 nm, Epot= -1.70410e+06 Fmax= 6.76528e+03, atom= 1703\n",
            "Step= 1069, Dmax= 6.9e-03 nm, Epot= -1.70414e+06 Fmax= 6.20204e+03, atom= 1703\n",
            "Step= 1070, Dmax= 8.3e-03 nm, Epot= -1.70416e+06 Fmax= 9.00946e+03, atom= 1703\n",
            "Step= 1071, Dmax= 1.0e-02 nm, Epot= -1.70420e+06 Fmax= 9.74825e+03, atom= 1703\n",
            "Step= 1072, Dmax= 1.2e-02 nm, Epot= -1.70420e+06 Fmax= 1.20274e+04, atom= 1703\n",
            "Step= 1073, Dmax= 1.4e-02 nm, Epot= -1.70422e+06 Fmax= 1.51109e+04, atom= 1703\n",
            "Step= 1074, Dmax= 1.7e-02 nm, Epot= -1.70421e+06 Fmax= 1.59361e+04, atom= 1703\rStep= 1075, Dmax= 8.6e-03 nm, Epot= -1.70436e+06 Fmax= 2.22064e+03, atom= 1703\n",
            "Step= 1076, Dmax= 1.0e-02 nm, Epot= -1.70437e+06 Fmax= 1.82441e+04, atom= 1704\n",
            "Step= 1077, Dmax= 1.2e-02 nm, Epot= -1.70453e+06 Fmax= 6.51402e+03, atom= 1703\n",
            "Step= 1078, Dmax= 1.5e-02 nm, Epot= -1.70435e+06 Fmax= 2.49565e+04, atom= 1703\rStep= 1079, Dmax= 7.4e-03 nm, Epot= -1.70457e+06 Fmax= 7.73153e+03, atom= 1703\n",
            "Step= 1080, Dmax= 8.9e-03 nm, Epot= -1.70459e+06 Fmax= 8.72962e+03, atom= 1703\n",
            "Step= 1081, Dmax= 1.1e-02 nm, Epot= -1.70461e+06 Fmax= 1.17138e+04, atom= 1703\n",
            "Step= 1082, Dmax= 1.3e-02 nm, Epot= -1.70463e+06 Fmax= 1.19122e+04, atom= 1703\n",
            "Step= 1083, Dmax= 1.5e-02 nm, Epot= -1.70461e+06 Fmax= 1.76341e+04, atom= 1703\rStep= 1084, Dmax= 7.7e-03 nm, Epot= -1.70475e+06 Fmax= 1.39074e+03, atom= 1703\n",
            "Step= 1085, Dmax= 9.3e-03 nm, Epot= -1.70481e+06 Fmax= 1.59989e+04, atom= 1703\n",
            "Step= 1086, Dmax= 1.1e-02 nm, Epot= -1.70501e+06 Fmax= 4.25278e+03, atom= 1703\n",
            "Step= 1087, Dmax= 1.3e-02 nm, Epot= -1.70490e+06 Fmax= 1.75784e+04, atom= 1703\rStep= 1088, Dmax= 6.7e-03 nm, Epot= -1.70503e+06 Fmax= 7.63939e+03, atom= 1703\n",
            "Step= 1089, Dmax= 8.0e-03 nm, Epot= -1.70507e+06 Fmax= 7.44698e+03, atom= 1703\n",
            "Step= 1090, Dmax= 9.6e-03 nm, Epot= -1.70509e+06 Fmax= 1.00833e+04, atom= 1703\n",
            "Step= 1091, Dmax= 1.2e-02 nm, Epot= -1.70512e+06 Fmax= 1.16589e+04, atom= 1703\n",
            "Step= 1092, Dmax= 1.4e-02 nm, Epot= -1.70511e+06 Fmax= 1.34303e+04, atom= 1703\rStep= 1093, Dmax= 6.9e-03 nm, Epot= -1.70521e+06 Fmax= 2.04764e+03, atom= 1703\n",
            "Step= 1094, Dmax= 8.3e-03 nm, Epot= -1.70526e+06 Fmax= 1.42354e+04, atom= 1704\n",
            "Step= 1095, Dmax= 9.9e-03 nm, Epot= -1.70536e+06 Fmax= 5.34761e+03, atom= 1703\n",
            "Step= 1096, Dmax= 1.2e-02 nm, Epot= -1.70528e+06 Fmax= 1.91935e+04, atom= 1703\rStep= 1097, Dmax= 6.0e-03 nm, Epot= -1.70540e+06 Fmax= 5.96839e+03, atom= 1703\n",
            "Step= 1098, Dmax= 7.2e-03 nm, Epot= -1.70543e+06 Fmax= 7.29022e+03, atom= 1703\n",
            "Step= 1099, Dmax= 8.6e-03 nm, Epot= -1.70546e+06 Fmax= 9.03129e+03, atom= 1703\n",
            "Step= 1100, Dmax= 1.0e-02 nm, Epot= -1.70548e+06 Fmax= 9.99001e+03, atom= 1703\n",
            "Step= 1101, Dmax= 1.2e-02 nm, Epot= -1.70549e+06 Fmax= 1.36092e+04, atom= 1703\n",
            "Step= 1102, Dmax= 1.5e-02 nm, Epot= -1.70551e+06 Fmax= 1.35706e+04, atom= 1703\n",
            "Step= 1103, Dmax= 1.8e-02 nm, Epot= -1.70546e+06 Fmax= 2.05853e+04, atom= 1703\rStep= 1104, Dmax= 8.9e-03 nm, Epot= -1.70565e+06 Fmax= 1.55298e+03, atom= 1703\n",
            "Step= 1105, Dmax= 1.1e-02 nm, Epot= -1.70565e+06 Fmax= 1.87582e+04, atom= 1703\rStep= 1106, Dmax= 5.3e-03 nm, Epot= -1.70572e+06 Fmax= 8.99279e+03, atom= 1703\n",
            "Step= 1107, Dmax= 6.4e-03 nm, Epot= -1.70579e+06 Fmax= 2.88638e+03, atom= 1703\n",
            "Step= 1108, Dmax= 7.7e-03 nm, Epot= -1.70582e+06 Fmax= 1.04726e+04, atom= 1703\n",
            "Step= 1109, Dmax= 9.2e-03 nm, Epot= -1.70590e+06 Fmax= 6.42552e+03, atom= 1703\n",
            "Step= 1110, Dmax= 1.1e-02 nm, Epot= -1.70587e+06 Fmax= 1.33184e+04, atom= 1703\rStep= 1111, Dmax= 5.5e-03 nm, Epot= -1.70594e+06 Fmax= 4.15512e+03, atom= 1703\n",
            "Step= 1112, Dmax= 6.6e-03 nm, Epot= -1.70597e+06 Fmax= 8.56590e+03, atom= 1703\n",
            "Step= 1113, Dmax= 8.0e-03 nm, Epot= -1.70602e+06 Fmax= 6.51388e+03, atom= 1703\n",
            "Step= 1114, Dmax= 9.6e-03 nm, Epot= -1.70602e+06 Fmax= 1.20540e+04, atom= 1703\n",
            "Step= 1115, Dmax= 1.1e-02 nm, Epot= -1.70607e+06 Fmax= 9.54403e+03, atom= 1703\n",
            "Step= 1116, Dmax= 1.4e-02 nm, Epot= -1.70603e+06 Fmax= 1.73374e+04, atom= 1703\rStep= 1117, Dmax= 6.9e-03 nm, Epot= -1.70615e+06 Fmax= 2.68012e+03, atom= 1703\n",
            "Step= 1118, Dmax= 8.3e-03 nm, Epot= -1.70617e+06 Fmax= 1.22952e+04, atom= 1703\n",
            "Step= 1119, Dmax= 9.9e-03 nm, Epot= -1.70627e+06 Fmax= 5.74791e+03, atom= 1703\n",
            "Step= 1120, Dmax= 1.2e-02 nm, Epot= -1.70621e+06 Fmax= 1.50399e+04, atom= 1703\rStep= 1121, Dmax= 6.0e-03 nm, Epot= -1.70631e+06 Fmax= 5.43591e+03, atom= 1703\n",
            "Step= 1122, Dmax= 7.1e-03 nm, Epot= -1.70633e+06 Fmax= 8.18043e+03, atom= 1703\n",
            "Step= 1123, Dmax= 8.6e-03 nm, Epot= -1.70636e+06 Fmax= 7.83521e+03, atom= 1703\n",
            "Step= 1124, Dmax= 1.0e-02 nm, Epot= -1.70637e+06 Fmax= 1.19220e+04, atom= 1703\n",
            "Step= 1125, Dmax= 1.2e-02 nm, Epot= -1.70641e+06 Fmax= 1.10019e+04, atom= 1703\n",
            "Step= 1126, Dmax= 1.5e-02 nm, Epot= -1.70638e+06 Fmax= 1.76021e+04, atom= 1703\rStep= 1127, Dmax= 7.4e-03 nm, Epot= -1.70651e+06 Fmax= 1.92120e+03, atom= 1703\n",
            "Step= 1128, Dmax= 8.9e-03 nm, Epot= -1.70653e+06 Fmax= 1.43730e+04, atom= 1703\n",
            "Step= 1129, Dmax= 1.1e-02 nm, Epot= -1.70668e+06 Fmax= 4.96282e+03, atom= 1703\n",
            "Step= 1130, Dmax= 1.3e-02 nm, Epot= -1.70659e+06 Fmax= 1.67910e+04, atom= 1703\rStep= 1131, Dmax= 6.4e-03 nm, Epot= -1.70671e+06 Fmax= 6.80584e+03, atom= 1703\n",
            "Step= 1132, Dmax= 7.7e-03 nm, Epot= -1.70675e+06 Fmax= 7.74552e+03, atom= 1703\n",
            "Step= 1133, Dmax= 9.2e-03 nm, Epot= -1.70676e+06 Fmax= 9.24446e+03, atom= 1703\n",
            "Step= 1134, Dmax= 1.1e-02 nm, Epot= -1.70679e+06 Fmax= 1.17840e+04, atom= 1703\n",
            "Step= 1135, Dmax= 1.3e-02 nm, Epot= -1.70680e+06 Fmax= 1.25331e+04, atom= 1703\n",
            "Step= 1136, Dmax= 1.6e-02 nm, Epot= -1.70678e+06 Fmax= 1.78948e+04, atom= 1703\rStep= 1137, Dmax= 8.0e-03 nm, Epot= -1.70692e+06 Fmax= 1.12518e+03, atom= 1703\n",
            "Step= 1138, Dmax= 9.6e-03 nm, Epot= -1.70700e+06 Fmax= 1.74390e+04, atom= 1703\n",
            "Step= 1139, Dmax= 1.1e-02 nm, Epot= -1.70723e+06 Fmax= 3.74438e+03, atom= 1703\n",
            "Step= 1140, Dmax= 1.4e-02 nm, Epot= -1.70713e+06 Fmax= 1.77982e+04, atom= 1703\rStep= 1141, Dmax= 6.9e-03 nm, Epot= -1.70726e+06 Fmax= 8.15220e+03, atom= 1704\n",
            "Step= 1142, Dmax= 8.3e-03 nm, Epot= -1.70730e+06 Fmax= 7.35210e+03, atom= 1703\n",
            "Step= 1143, Dmax= 9.9e-03 nm, Epot= -1.70730e+06 Fmax= 1.07083e+04, atom= 1703\n",
            "Step= 1144, Dmax= 1.2e-02 nm, Epot= -1.70734e+06 Fmax= 1.16846e+04, atom= 1703\n",
            "Step= 1145, Dmax= 1.4e-02 nm, Epot= -1.70732e+06 Fmax= 1.41240e+04, atom= 1703\rStep= 1146, Dmax= 7.1e-03 nm, Epot= -1.70743e+06 Fmax= 2.45086e+03, atom= 1703\n",
            "Step= 1147, Dmax= 8.6e-03 nm, Epot= -1.70745e+06 Fmax= 1.43869e+04, atom= 1704\n",
            "Step= 1148, Dmax= 1.0e-02 nm, Epot= -1.70755e+06 Fmax= 5.80174e+03, atom= 1703\n",
            "Step= 1149, Dmax= 1.2e-02 nm, Epot= -1.70746e+06 Fmax= 1.94355e+04, atom= 1703\rStep= 1150, Dmax= 6.2e-03 nm, Epot= -1.70759e+06 Fmax= 5.79526e+03, atom= 1703\n",
            "Step= 1151, Dmax= 7.4e-03 nm, Epot= -1.70762e+06 Fmax= 7.86016e+03, atom= 1703\n",
            "Step= 1152, Dmax= 8.9e-03 nm, Epot= -1.70765e+06 Fmax= 8.92602e+03, atom= 1703\n",
            "Step= 1153, Dmax= 1.1e-02 nm, Epot= -1.70766e+06 Fmax= 1.06331e+04, atom= 1703\n",
            "Step= 1154, Dmax= 1.3e-02 nm, Epot= -1.70767e+06 Fmax= 1.36533e+04, atom= 1703\n",
            "Step= 1155, Dmax= 1.5e-02 nm, Epot= -1.70767e+06 Fmax= 1.42803e+04, atom= 1703\rStep= 1156, Dmax= 7.7e-03 nm, Epot= -1.70779e+06 Fmax= 1.76161e+03, atom= 1703\n",
            "Step= 1157, Dmax= 9.2e-03 nm, Epot= -1.70784e+06 Fmax= 1.63733e+04, atom= 1704\n",
            "Step= 1158, Dmax= 1.1e-02 nm, Epot= -1.70796e+06 Fmax= 5.64476e+03, atom= 1704\n",
            "Step= 1159, Dmax= 1.3e-02 nm, Epot= -1.70783e+06 Fmax= 2.22727e+04, atom= 1703\rStep= 1160, Dmax= 6.6e-03 nm, Epot= -1.70800e+06 Fmax= 7.15028e+03, atom= 1703\n",
            "Step= 1161, Dmax= 8.0e-03 nm, Epot= -1.70803e+06 Fmax= 7.61430e+03, atom= 1703\n",
            "Step= 1162, Dmax= 9.5e-03 nm, Epot= -1.70804e+06 Fmax= 1.06916e+04, atom= 1703\n",
            "Step= 1163, Dmax= 1.1e-02 nm, Epot= -1.70807e+06 Fmax= 1.05336e+04, atom= 1703\n",
            "Step= 1164, Dmax= 1.4e-02 nm, Epot= -1.70805e+06 Fmax= 1.58998e+04, atom= 1703\rStep= 1165, Dmax= 6.9e-03 nm, Epot= -1.70816e+06 Fmax= 1.50485e+03, atom= 1703\n",
            "Step= 1166, Dmax= 8.2e-03 nm, Epot= -1.70821e+06 Fmax= 1.37646e+04, atom= 1703\n",
            "Step= 1167, Dmax= 9.9e-03 nm, Epot= -1.70835e+06 Fmax= 4.26119e+03, atom= 1703\n",
            "Step= 1168, Dmax= 1.2e-02 nm, Epot= -1.70829e+06 Fmax= 1.58686e+04, atom= 1703\rStep= 1169, Dmax= 5.9e-03 nm, Epot= -1.70838e+06 Fmax= 6.58237e+03, atom= 1703\n",
            "Step= 1170, Dmax= 7.1e-03 nm, Epot= -1.70842e+06 Fmax= 6.90586e+03, atom= 1703\n",
            "Step= 1171, Dmax= 8.6e-03 nm, Epot= -1.70844e+06 Fmax= 8.84507e+03, atom= 1703\n",
            "Step= 1172, Dmax= 1.0e-02 nm, Epot= -1.70847e+06 Fmax= 1.06162e+04, atom= 1703\n",
            "Step= 1173, Dmax= 1.2e-02 nm, Epot= -1.70847e+06 Fmax= 1.19450e+04, atom= 1703\n",
            "Step= 1174, Dmax= 1.5e-02 nm, Epot= -1.70847e+06 Fmax= 1.62018e+04, atom= 1703\rStep= 1175, Dmax= 7.4e-03 nm, Epot= -1.70858e+06 Fmax= 8.03661e+02, atom= 1699\n",
            "\n",
            "writing lowest energy coordinates.\n",
            "\n",
            "Steepest Descents converged to Fmax < 1000 in 1176 steps\n",
            "Potential Energy  = -1.7085826e+06\n",
            "Maximum force     =  8.0366052e+02 on atom 1699\n",
            "Norm of force     =  1.9286574e+01\n",
            "\n",
            "GROMACS reminds you: \"The physical chemists never use their eyes and are most lamentably lacking in chemical culture. It is essential to cast out from our midst, root and branch, this physical element and return to our laboratories.\" (Henry Edward Armstrong)\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "%%bash\n",
        "source /content/gromacs/bin/GMXRC\n",
        "gmx genrestr -f ligand.gro -o posre_ligand.itp -fc 1000 1000 1000 <<< 0\n",
        "sed -i '/Include water topology/i \\; Include Position restraint file' topol.top\n",
        "sed -i '/Include water topology/i \\#ifdef POSRES' topol.top\n",
        "sed -i '/Include water topology/i \\#include \"posre_ligand.itp\"' topol.top\n",
        "sed -i '/Include water topology/i \\#endif' topol.top\n",
        "sed -i '/Include water topology/i \\ ' topol.top\n",
        "printf \"%s\\n\" \"1 | 13\" \"q\" |  gmx make_ndx -f em.gro -o index.ndx \n"
      ],
      "metadata": {
        "id": "LUq-tn0i-9Sz",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "b9e7f77d-e1fa-4b3f-99dc-051ae40183e4"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Select group to position restrain\n",
            "Selected 0: 'System'\n",
            "Going to read 0 old index file(s)\n",
            "Analysing residue names:\n",
            "There are:   163    Protein residues\n",
            "There are:     1      Other residues\n",
            "There are: 30684      Water residues\n",
            "There are:   178        Ion residues\n",
            "Analysing Protein...\n",
            "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n",
            "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n",
            "\n",
            "  0 System              : 93935 atoms\n",
            "  1 Protein             :  1695 atoms\n",
            "  2 Protein-H           :  1301 atoms\n",
            "  3 C-alpha             :   163 atoms\n",
            "  4 Backbone            :   489 atoms\n",
            "  5 MainChain           :   653 atoms\n",
            "  6 MainChain+Cb        :   805 atoms\n",
            "  7 MainChain+H         :   815 atoms\n",
            "  8 SideChain           :   880 atoms\n",
            "  9 SideChain-H         :   648 atoms\n",
            " 10 Prot-Masses         :  1695 atoms\n",
            " 11 non-Protein         : 92240 atoms\n",
            " 12 Other               :    10 atoms\n",
            " 13 JZ4                 :    10 atoms\n",
            " 14 NA                  :    86 atoms\n",
            " 15 CL                  :    92 atoms\n",
            " 16 Water               : 92052 atoms\n",
            " 17 SOL                 : 92052 atoms\n",
            " 18 non-Water           :  1883 atoms\n",
            " 19 Ion                 :   178 atoms\n",
            " 20 JZ4                 :    10 atoms\n",
            " 21 NA                  :    86 atoms\n",
            " 22 CL                  :    92 atoms\n",
            " 23 Water_and_ions      : 92230 atoms\n",
            "\n",
            " nr : group      '!': not  'name' nr name   'splitch' nr    Enter: list groups\n",
            " 'a': atom       '&': and  'del' nr         'splitres' nr   'l': list residues\n",
            " 't': atom type  '|': or   'keep' nr        'splitat' nr    'h': help\n",
            " 'r': residue              'res' nr         'chain' char\n",
            " \"name\": group             'case': case sensitive           'q': save and quit\n",
            " 'ri': residue index\n",
            "\n",
            "> \n",
            "Copied index group 1 'Protein'\n",
            "Copied index group 13 'JZ4'\n",
            "Merged two groups with OR: 1695 10 -> 1705\n",
            "\n",
            " 24 Protein_JZ4         :  1705 atoms\n",
            "\n",
            "> \n"
          ]
        },
        {
          "output_type": "stream",
          "name": "stderr",
          "text": [
            "                     :-) GROMACS - gmx genrestr, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx genrestr, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx genrestr -f ligand.gro -o posre_ligand.itp -fc 1000 1000 1000\n",
            "\n",
            "\n",
            "Reading structure file\n",
            "Group     0 (         System) has    10 elements\n",
            "Group     1 (          Other) has    10 elements\n",
            "Group     2 (            JZ4) has    10 elements\n",
            "Select a group: \n",
            "GROMACS reminds you: \"You wouldn't walk into a chemistry lab and mix two clear liquids together just because they look pretty much the same, would you?\" (Justin Lemkul)\n",
            "\n",
            "                     :-) GROMACS - gmx make_ndx, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx make_ndx, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx make_ndx -f em.gro -o index.ndx\n",
            "\n",
            "\n",
            "Reading structure file\n",
            "\n",
            "GROMACS reminds you: \"You wouldn't walk into a chemistry lab and mix two clear liquids together just because they look pretty much the same, would you?\" (Justin Lemkul)\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!chmod a+x *\n",
        "!sudo apt install vim -y"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "kv1_JBwbltwt",
        "outputId": "c6adb05a-6897-46e4-e05c-d0edf6f397ad"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Reading package lists... Done\n",
            "Building dependency tree       \n",
            "Reading state information... Done\n",
            "vim is already the newest version (2:8.0.1453-1ubuntu1.8).\n",
            "The following package was automatically installed and is no longer required:\n",
            "  libnvidia-common-460\n",
            "Use 'sudo apt autoremove' to remove it.\n",
            "0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "%%bash\n",
        "source /content/gromacs/bin/GMXRC\n",
        "gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr -r em.gro -maxwarn 2\n",
        "gmx mdrun -deffnm nvt -v\n",
        "\n",
        "gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt-1000.tpr -r em.gro -maxwarn 2\n",
        "gmx mdrun -deffnm npt-1000  -v\n",
        "\n"
      ],
      "metadata": {
        "id": "U5lyA7av-9Wu",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "06c6bc5a-2289-4efd-e5e2-0e618d1b9ab9"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K\n",
            "Calculated rlist for 1x1 atom pair-list as 1.009 nm, buffer size 0.009 nm\n",
            "Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm\n",
            "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
            "Calculating fourier grid dimensions for X Y Z\n",
            "Using a fourier grid of 64x64x64, spacing 0.154 0.154 0.154\n",
            "This run will generate roughly 117 Mb of data\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K\n",
            "Calculated rlist for 1x1 atom pair-list as 1.009 nm, buffer size 0.009 nm\n",
            "Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm\n",
            "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
            "Calculating fourier grid dimensions for X Y Z\n",
            "Using a fourier grid of 64x64x64, spacing 0.154 0.154 0.154\n",
            "This run will generate roughly 30 Mb of data\n"
          ]
        },
        {
          "output_type": "stream",
          "name": "stderr",
          "text": [
            "                      :-) GROMACS - gmx grompp, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx grompp, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr -r em.gro -maxwarn 2\n",
            "\n",
            "Ignoring obsolete mdp entry 'title'\n",
            "Ignoring obsolete mdp entry 'ns_type'\n",
            "\n",
            "NOTE 1 [file nvt.mdp]:\n",
            "  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note\n",
            "  that with the Verlet scheme, nstlist has no effect on the accuracy of\n",
            "  your simulation.\n",
            "\n",
            "Setting the LD random seed to 1962798777\n",
            "Generated 210 of the 2556 non-bonded parameter combinations\n",
            "Excluding 3 bonded neighbours molecule type 'Protein_chain_A'\n",
            "Excluding 3 bonded neighbours molecule type 'JZ4'\n",
            "Excluding 2 bonded neighbours molecule type 'SOL'\n",
            "Excluding 1 bonded neighbours molecule type 'NA'\n",
            "Excluding 1 bonded neighbours molecule type 'CL'\n",
            "\n",
            "WARNING 1 [file topol.top, line 11015]:\n",
            "  The GROMOS force fields have been parametrized with a physically\n",
            "  incorrect multiple-time-stepping scheme for a twin-range cut-off. When\n",
            "  used with a single-range cut-off (or a correct Trotter\n",
            "  multiple-time-stepping scheme), physical properties, such as the density,\n",
            "  might differ from the intended values. Since there are researchers\n",
            "  actively working on validating GROMOS with modern integrators we have not\n",
            "  yet removed the GROMOS force fields, but you should be aware of these\n",
            "  issues and check if molecules in your system are affected before\n",
            "  proceeding. Further information is available at\n",
            "  https://redmine.gromacs.org/issues/2884 , and a longer explanation of our\n",
            "  decision to remove physically incorrect algorithms can be found at\n",
            "  https://doi.org/10.26434/chemrxiv.11474583.v1 .\n",
            "\n",
            "Setting gen_seed to -1669605905\n",
            "Velocities were taken from a Maxwell distribution at 310 K\n",
            "Number of degrees of freedom in T-Coupling group Protein_JZ4 is 3389.95\n",
            "Number of degrees of freedom in T-Coupling group Water_and_ions is 184635.05\n",
            "\n",
            "NOTE 2 [file nvt.mdp]:\n",
            "  Removing center of mass motion in the presence of position restraints\n",
            "  might cause artifacts. When you are using position restraints to\n",
            "  equilibrate a macro-molecule, the artifacts are usually negligible.\n",
            "\n",
            "Estimate for the relative computational load of the PME mesh part: 0.23\n",
            "\n",
            "There were 2 notes\n",
            "\n",
            "There was 1 warning\n",
            "\n",
            "GROMACS reminds you: \"I'm not interrupting you, I'm putting our conversation in full-duplex mode.\" (Antone Roundy)\n",
            "\n",
            "                      :-) GROMACS - gmx mdrun, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx mdrun, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx mdrun -deffnm nvt -v\n",
            "\n",
            "Reading file nvt.tpr, VERSION 2020.6 (single precision)\n",
            "Changing nstlist from 5 to 80, rlist from 1 to 1.147\n",
            "\n",
            "1 GPU selected for this run.\n",
            "Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:\n",
            "  PP:0,PME:0\n",
            "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
            "PP task will update and constrain coordinates on the CPU\n",
            "PME tasks will do all aspects on the GPU\n",
            "Using 1 MPI thread\n",
            "\n",
            "Non-default thread affinity set, disabling internal thread affinity\n",
            "\n",
            "Using 2 OpenMP threads \n",
            "\n",
            "starting mdrun 'Protein in water'\n",
            "50000 steps,    100.0 ps.\n",
            "\rstep 0\rstep 100, remaining wall clock time:   249 s          \rstep 200, remaining wall clock time:   214 s          \rstep 300, remaining wall clock time:   200 s          \rstep 400, remaining wall clock time:   195 s          \rstep 500, remaining wall clock time:   186 s          \rstep 600, remaining wall clock time:   183 s          \rstep 700, remaining wall clock time:   179 s          \rstep 800, remaining wall clock time:   178 s          \rstep 900, remaining wall clock time:   176 s          \rstep 1000, remaining wall clock time:   175 s          \rstep 1100, remaining wall clock time:   173 s          \rstep 1200, remaining wall clock time:   173 s          \rstep 1300, remaining wall clock time:   171 s          \rstep 1400, remaining wall clock time:   170 s          \rstep 1520: timed with pme grid 64 64 64, coulomb cutoff 1.000: 600.1 M-cycles\n",
            "\rstep 1680: timed with pme grid 56 56 56, coulomb cutoff 1.099: 644.3 M-cycles\n",
            "\rstep 1840: timed with pme grid 48 48 48, coulomb cutoff 1.282: 724.2 M-cycles\n",
            "\rstep 2000: timed with pme grid 52 52 52, coulomb cutoff 1.184: 665.3 M-cycles\n",
            "\rstep 2160: timed with pme grid 56 56 56, coulomb cutoff 1.099: 658.1 M-cycles\n",
            "\rstep 2320: timed with pme grid 60 60 60, coulomb cutoff 1.026: 563.5 M-cycles\n",
            "\rstep 2480: timed with pme grid 64 64 64, coulomb cutoff 1.000: 554.9 M-cycles\n",
            "\rstep 2640: timed with pme grid 60 60 60, coulomb cutoff 1.026: 575.5 M-cycles\n",
            "\rstep 2800: timed with pme grid 64 64 64, coulomb cutoff 1.000: 557.9 M-cycles\n",
            "\r              optimal pme grid 64 64 64, coulomb cutoff 1.000\n",
            "\rstep 2900, remaining wall clock time:   213 s          \rstep 3000, remaining wall clock time:   211 s          \rstep 3100, remaining wall clock time:   208 s          \rstep 3200, remaining wall clock time:   206 s          \rstep 3300, remaining wall clock time:   204 s          \rstep 3400, remaining wall clock time:   202 s          \rstep 3500, remaining wall clock time:   200 s          \rstep 3600, remaining wall clock time:   198 s          \rstep 3700, remaining wall clock time:   196 s          \rstep 3800, remaining wall clock time:   195 s          \rstep 3900, remaining wall clock time:   193 s          \rstep 4000, remaining wall clock time:   193 s          \rstep 4100, remaining wall clock time:   191 s          \rstep 4200, remaining wall clock time:   190 s          \rstep 4300, remaining wall clock time:   188 s          \rstep 4400, remaining wall clock time:   187 s          \rstep 4500, remaining wall clock time:   186 s          \rstep 4600, 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clock time:     1 s          \rstep 49600, remaining wall clock time:     1 s          \rstep 49700, remaining wall clock time:     1 s          \rstep 49800, remaining wall clock time:     0 s          \rstep 49900, remaining wall clock time:     0 s          \n",
            "Writing final coordinates.\n",
            "\rstep 50000, remaining wall clock time:     0 s          \n",
            "NOTE: 12 % of the run time was spent in pair search,\n",
            "      you might want to increase nstlist (this has no effect on accuracy)\n",
            "\n",
            "               Core t (s)   Wall t (s)        (%)\n",
            "       Time:      347.658      173.830      200.0\n",
            "                 (ns/day)    (hour/ns)\n",
            "Performance:       49.705        0.483\n",
            "\n",
            "GROMACS reminds you: \"An expert is a person who has made all the mistakes that can be made in a very narrow field.\" (Niels Bohr)\n",
            "\n",
            "                      :-) GROMACS - gmx grompp, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx grompp, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt-1000.tpr -r em.gro -maxwarn 2\n",
            "\n",
            "Ignoring obsolete mdp entry 'title'\n",
            "Ignoring obsolete mdp entry 'ns_type'\n",
            "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
            "\n",
            "NOTE 1 [file npt.mdp]:\n",
            "  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note\n",
            "  that with the Verlet scheme, nstlist has no effect on the accuracy of\n",
            "  your simulation.\n",
            "\n",
            "Setting the LD random seed to -1751130369\n",
            "Generated 210 of the 2556 non-bonded parameter combinations\n",
            "Excluding 3 bonded neighbours molecule type 'Protein_chain_A'\n",
            "Excluding 3 bonded neighbours molecule type 'JZ4'\n",
            "Excluding 2 bonded neighbours molecule type 'SOL'\n",
            "Excluding 1 bonded neighbours molecule type 'NA'\n",
            "Excluding 1 bonded neighbours molecule type 'CL'\n",
            "\n",
            "WARNING 1 [file topol.top, line 11015]:\n",
            "  The GROMOS force fields have been parametrized with a physically\n",
            "  incorrect multiple-time-stepping scheme for a twin-range cut-off. When\n",
            "  used with a single-range cut-off (or a correct Trotter\n",
            "  multiple-time-stepping scheme), physical properties, such as the density,\n",
            "  might differ from the intended values. Since there are researchers\n",
            "  actively working on validating GROMOS with modern integrators we have not\n",
            "  yet removed the GROMOS force fields, but you should be aware of these\n",
            "  issues and check if molecules in your system are affected before\n",
            "  proceeding. Further information is available at\n",
            "  https://redmine.gromacs.org/issues/2884 , and a longer explanation of our\n",
            "  decision to remove physically incorrect algorithms can be found at\n",
            "  https://doi.org/10.26434/chemrxiv.11474583.v1 .\n",
            "\n",
            "\n",
            "NOTE 2 [file topol.top, line 11015]:\n",
            "  You are combining position restraints with Parrinello-Rahman pressure\n",
            "  coupling, which can lead to instabilities. If you really want to combine\n",
            "  position restraints with pressure coupling, we suggest to use Berendsen\n",
            "  pressure coupling instead.\n",
            "\n",
            "The center of mass of the position restraint coord's is  4.926  4.923  4.907\n",
            "The center of mass of the position restraint coord's is  4.926  4.923  4.907\n",
            "Number of degrees of freedom in T-Coupling group Protein_JZ4 is 3389.95\n",
            "Number of degrees of freedom in T-Coupling group Water_and_ions is 184635.05\n",
            "\n",
            "NOTE 3 [file npt.mdp]:\n",
            "  Removing center of mass motion in the presence of position restraints\n",
            "  might cause artifacts. When you are using position restraints to\n",
            "  equilibrate a macro-molecule, the artifacts are usually negligible.\n",
            "\n",
            "Reading Coordinates, Velocities and Box size from old trajectory\n",
            "Will read whole trajectory\n",
            "\rLast frame         -1 time  100.000   \n",
            "Using frame at t = 100 ps\n",
            "Starting time for run is 0 ps\n",
            "Estimate for the relative computational load of the PME mesh part: 0.23\n",
            "\n",
            "There were 3 notes\n",
            "\n",
            "There was 1 warning\n",
            "\n",
            "GROMACS reminds you: \"An expert is a person who has made all the mistakes that can be made in a very narrow field.\" (Niels Bohr)\n",
            "\n",
            "                      :-) GROMACS - gmx mdrun, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx mdrun, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx mdrun -deffnm npt-1000 -v\n",
            "\n",
            "Reading file npt-1000.tpr, VERSION 2020.6 (single precision)\n",
            "Changing nstlist from 5 to 80, rlist from 1 to 1.147\n",
            "\n",
            "1 GPU selected for this run.\n",
            "Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:\n",
            "  PP:0,PME:0\n",
            "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
            "PP task will update and constrain coordinates on the CPU\n",
            "PME tasks will do all aspects on the GPU\n",
            "Using 1 MPI thread\n",
            "\n",
            "Non-default thread affinity set, disabling internal thread affinity\n",
            "\n",
            "Using 2 OpenMP threads \n",
            "\n",
            "starting mdrun 'Protein in water'\n",
            "50000 steps,    100.0 ps.\n",
            "\rstep 0\rstep 100, remaining wall clock time:   258 s          \rstep 200, remaining wall clock time:   226 s          \rstep 300, remaining wall clock time:   208 s          \rstep 400, remaining wall clock time:   207 s          \rstep 500, remaining wall clock time:   200 s          \rstep 600, remaining wall clock time:   194 s          \rstep 700, remaining wall clock time:   191 s          \rstep 800, remaining wall clock time:   191 s          \rstep 900, remaining wall clock time:   188 s          \rstep 1000, remaining wall clock time:   186 s          \rstep 1100, remaining wall clock time:   184 s          \rstep 1200, remaining wall clock time:   184 s          \rstep 1300, remaining wall clock time:   182 s          \rstep 1440: timed with pme grid 64 64 64, coulomb cutoff 1.000: 608.1 M-cycles\n",
            "\rstep 1600: timed with pme grid 56 56 56, coulomb cutoff 1.099: 662.4 M-cycles\n",
            "\rstep 1760: timed with pme grid 48 48 48, coulomb cutoff 1.282: 751.4 M-cycles\n",
            "\rstep 1920: timed with pme grid 52 52 52, coulomb cutoff 1.184: 716.9 M-cycles\n",
            "\rstep 2080: timed with pme grid 56 56 56, coulomb cutoff 1.099: 707.2 M-cycles\n",
            "\rstep 2240: timed with pme grid 60 60 60, coulomb cutoff 1.026: 624.5 M-cycles\n",
            "\rstep 2400: timed with pme grid 64 64 64, coulomb cutoff 1.000: 599.8 M-cycles\n",
            "\r              optimal pme grid 64 64 64, coulomb cutoff 1.000\n",
            "\rstep 2500, remaining wall clock time:   235 s          \rstep 2600, remaining wall clock time:   232 s          \rstep 2700, remaining wall clock time:   229 s          \rstep 2800, remaining wall clock time:   226 s          \rstep 2900, remaining wall clock time:   224 s          \rstep 3000, remaining wall clock time:   222 s          \rstep 3100, remaining wall clock time:   219 s          \rstep 3200, remaining wall clock time:   217 s          \rstep 3300, remaining wall clock time:   215 s          \rstep 3400, remaining wall clock time:   213 s          \rstep 3500, remaining wall clock time:   211 s          \rstep 3600, remaining wall clock time:   210 s          \rstep 3700, remaining wall clock time:   208 s          \rstep 3800, remaining wall clock time:   206 s          \rstep 3900, remaining wall clock time:   205 s          \rstep 4000, remaining wall clock time:   204 s          \rstep 4100, remaining wall clock time:   202 s          \rstep 4200, 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            "Writing final coordinates.\n",
            "\rstep 50000, remaining wall clock time:     0 s          \n",
            "NOTE: 12 % of the run time was spent in pair search,\n",
            "      you might want to increase nstlist (this has no effect on accuracy)\n",
            "\n",
            "               Core t (s)   Wall t (s)        (%)\n",
            "       Time:      369.461      184.731      200.0\n",
            "                 (ns/day)    (hour/ns)\n",
            "Performance:       46.772        0.513\n",
            "\n",
            "GROMACS reminds you: \"It was something to at least have a choice of nightmares\" (Joseph Conrad)\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "%%bash\n",
        "source /content/gromacs/bin/GMXRC\n",
        "\n",
        "arr=(*_*_*_*.itp) && echo \"${arr[0]}\"\n",
        "\n",
        "filename=${arr[0]}\n",
        "\n",
        "if [ -f \"${filename}\" ]\n",
        "\n",
        "then\n",
        "\n",
        "vim -c \":%s/1000  1000  1000/100     100     100/g\" -c wq <<< E ${arr[0]}\n",
        "vim -c \":%s/1000  1000  1000/100     100     100/g\" -c wq <<< E ${arr[1]}\n",
        "vim -c \":%s/1000       1000       1000/100     100     100/g\" -c wq <<< E posre_ligand.itp\n",
        "\n",
        "gmx grompp -f npt.mdp -c npt-1000.gro -t npt-1000.cpt -p topol.top -n index.ndx -o npt-100.tpr -r em.gro -maxwarn 2 \n",
        "gmx mdrun -deffnm npt-100  -v\n",
        "vim -c \":%s/100     100     100/10     10     10/g\" -c wq <<< E ${arr[0]}\n",
        "vim -c \":%s/100     100     100/10     10     10/g\" -c wq <<< E ${arr[1]}\n",
        "vim -c \":%s/100     100     100/10     10     10/g\" -c wq <<< E posre_ligand.itp\n",
        "\n",
        "gmx grompp -f npt.mdp -c npt-100.gro -t npt-100.cpt -p topol.top -n index.ndx -o npt-10.tpr -r em.gro -maxwarn 2 \n",
        "gmx mdrun -deffnm npt-10  -v\n",
        "vim -c \":%s/10     10     10/1     1     1/g\" -c wq <<< E ${arr[0]}\n",
        "vim -c \":%s/10     10     10/1     1     1/g\" -c wq <<< E ${arr[1]}\n",
        "vim -c \":%s/10     10     10/1     1     1/g\" -c wq <<< E posre_ligand.itp\n",
        "\n",
        "\n",
        "else \n",
        "vim -c \":%s/1000  1000  1000/100     100     100/g\" -c wq <<< E posre.itp\n",
        "vim -c \":%s/1000       1000       1000/100     100     100/g\" -c wq <<< E posre_ligand.itp\n",
        "\n",
        "gmx grompp -f npt.mdp -c npt-1000.gro -t npt-1000.cpt -p topol.top -n index.ndx -o npt-100.tpr -r em.gro -maxwarn 2 \n",
        "gmx mdrun -deffnm npt-100  -v\n",
        "vim -c \":%s/100     100     100/10     10     10/g\" -c wq <<< E posre.itp\n",
        "vim -c \":%s/100     100     100/10     10     10/g\" -c wq <<< E posre_ligand.itp\n",
        "\n",
        "gmx grompp -f npt.mdp -c npt-100.gro -t npt-100.cpt -p topol.top -n index.ndx -o npt-10.tpr -r em.gro -maxwarn 2 \n",
        "gmx mdrun -deffnm npt-10  -v\n",
        "vim -c \":%s/10     10     10/1     1     1/g\" -c wq <<< E posre.itp\n",
        "vim -c \":%s/10     10     10/1     1     1/g\" -c wq <<< E posre_ligand.itp\n",
        "fi\n",
        "\n",
        "\n",
        "gmx grompp -f npt.mdp -c npt-10.gro -t npt-10.cpt -p topol.top -n index.ndx -o npt-1.tpr -r em.gro -maxwarn 2 \n",
        "gmx mdrun -deffnm npt-1 -v\n",
        "\n",
        "vim -c \":%s/define/;define/g\" -c wq <<< E npt.mdp\n",
        "\n",
        "gmx grompp -f npt.mdp -c npt-1.gro -t npt-1.cpt -p topol.top -n index.ndx -o npt.tpr -r em.gro -maxwarn 2\n",
        "gmx mdrun -deffnm npt -v"
      ],
      "metadata": {
        "id": "oBXxpTLiBvuo",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "7f9f3381-ca77-4ddc-882a-fcaf7b0367ae"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "posre_Protein_chain_A.itp\n",
            "\u001b[?2004h\u001b7\u001b[?47h\u001b[?1h\u001b=\u001b[?2004h\u001b[1;24r\u001b[?12h\u001b[?12l\u001b[29m\u001b[m\u001b[H\u001b[2J\u001b[?25l\u001b[24;1H\"posre_Protein_chain_A.itp\" 1308L, 36701C\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mError detected while processing command line:\u001b[m\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mE486: Pattern not found: 1000  1000  1000\u001b[?2004l\u001b[m\r\r\n",
            "\"posre_Protein_chain_A.itp\" 1308L, 36701C written\r\r\n",
            "\u001b[?2004l\u001b[?1l\u001b>\u001b[?25h\u001b[2J\u001b[?47l\u001b8\u001b[?2004h\u001b7\u001b[?47h\u001b[?1h\u001b=\u001b[?2004h\u001b[1;24r\u001b[?12h\u001b[?12l\u001b[29m\u001b[m\u001b[H\u001b[2J\u001b[?25l\u001b[24;1H\"topol_Protein_chain_A.itp\" 10983L, 384738C\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mError detected while processing command line:\u001b[m\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mE486: Pattern not found: 1000  1000  1000\u001b[?2004l\u001b[m\r\r\n",
            "\"topol_Protein_chain_A.itp\" 10983L, 384738C written\r\r\n",
            "\u001b[?2004l\u001b[?1l\u001b>\u001b[?25h\u001b[2J\u001b[?47l\u001b8\u001b[?2004h\u001b7\u001b[?47h\u001b[?1h\u001b=\u001b[?2004h\u001b[1;24r\u001b[?12h\u001b[?12l\u001b[29m\u001b[m\u001b[H\u001b[2J\u001b[?25l\u001b[24;1H\"posre_ligand.itp\" 14L, 451C\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mError detected while processing command line:\u001b[m\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mE486: Pattern not found: 1000       1000       1000\u001b[?2004l\u001b[m\r\r\n",
            "\"posre_ligand.itp\" 14L, 451C written\r\r\n",
            "\u001b[?2004l\u001b[?1l\u001b>\u001b[?25h\u001b[2J\u001b[?47l\u001b8turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K\n",
            "Calculated rlist for 1x1 atom pair-list as 1.010 nm, buffer size 0.010 nm\n",
            "Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm\n",
            "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
            "Calculating fourier grid dimensions for X Y Z\n",
            "Using a fourier grid of 64x64x64, spacing 0.152 0.152 0.156\n",
            "This run will generate roughly 30 Mb of data\n",
            "\u001b[?2004h\u001b7\u001b[?47h\u001b[?1h\u001b=\u001b[?2004h\u001b[1;24r\u001b[?12h\u001b[?12l\u001b[29m\u001b[m\u001b[H\u001b[2J\u001b[?25l\u001b[24;1H\"posre_Protein_chain_A.itp\" 1308L, 36701C\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mError detected while processing command line:\u001b[m\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mE486: Pattern not found: 100     100     100\u001b[?2004l\u001b[m\r\r\n",
            "\"posre_Protein_chain_A.itp\" 1308L, 36701C written\r\r\n",
            "\u001b[?2004l\u001b[?1l\u001b>\u001b[?25h\u001b[2J\u001b[?47l\u001b8\u001b[?2004h\u001b7\u001b[?47h\u001b[?1h\u001b=\u001b[?2004h\u001b[1;24r\u001b[?12h\u001b[?12l\u001b[29m\u001b[m\u001b[H\u001b[2J\u001b[?25l\u001b[24;1H\"topol_Protein_chain_A.itp\" 10983L, 384738C\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mError detected while processing command line:\u001b[m\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mE486: Pattern not found: 100     100     100\u001b[?2004l\u001b[m\r\r\n",
            "\"topol_Protein_chain_A.itp\" 10983L, 384738C written\r\r\n",
            "\u001b[?2004l\u001b[?1l\u001b>\u001b[?25h\u001b[2J\u001b[?47l\u001b8\u001b[?2004h\u001b7\u001b[?47h\u001b[?1h\u001b=\u001b[?2004h\u001b[1;24r\u001b[?12h\u001b[?12l\u001b[29m\u001b[m\u001b[H\u001b[2J\u001b[?25l\u001b[24;1H\"posre_ligand.itp\" 14L, 451C\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mError detected while processing command line:\u001b[m\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mE486: Pattern not found: 100     100     100\u001b[?2004l\u001b[m\r\r\n",
            "\"posre_ligand.itp\" 14L, 451C written\r\r\n",
            "\u001b[?2004l\u001b[?1l\u001b>\u001b[?25h\u001b[2J\u001b[?47l\u001b8turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K\n",
            "Calculated rlist for 1x1 atom pair-list as 1.010 nm, buffer size 0.010 nm\n",
            "Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm\n",
            "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
            "Calculating fourier grid dimensions for X Y Z\n",
            "Using a fourier grid of 64x64x64, spacing 0.154 0.154 0.153\n",
            "This run will generate roughly 30 Mb of data\n",
            "\u001b[?2004h\u001b7\u001b[?47h\u001b[?1h\u001b=\u001b[?2004h\u001b[1;24r\u001b[?12h\u001b[?12l\u001b[29m\u001b[m\u001b[H\u001b[2J\u001b[?25l\u001b[24;1H\"posre_Protein_chain_A.itp\" 1308L, 36701C\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mError detected while processing command line:\u001b[m\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mE486: Pattern not found: 10     10     10\u001b[?2004l\u001b[m\r\r\n",
            "\"posre_Protein_chain_A.itp\" 1308L, 36701C written\r\r\n",
            "\u001b[?2004l\u001b[?1l\u001b>\u001b[?25h\u001b[2J\u001b[?47l\u001b8\u001b[?2004h\u001b7\u001b[?47h\u001b[?1h\u001b=\u001b[?2004h\u001b[1;24r\u001b[?12h\u001b[?12l\u001b[29m\u001b[m\u001b[H\u001b[2J\u001b[?25l\u001b[24;1H\"topol_Protein_chain_A.itp\" 10983L, 384738C\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mError detected while processing command line:\u001b[m\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mE486: Pattern not found: 10     10     10\u001b[?2004l\u001b[m\r\r\n",
            "\"topol_Protein_chain_A.itp\" 10983L, 384738C written\r\r\n",
            "\u001b[?2004l\u001b[?1l\u001b>\u001b[?25h\u001b[2J\u001b[?47l\u001b8\u001b[?2004h\u001b7\u001b[?47h\u001b[?1h\u001b=\u001b[?2004h\u001b[1;24r\u001b[?12h\u001b[?12l\u001b[29m\u001b[m\u001b[H\u001b[2J\u001b[?25l\u001b[24;1H\"posre_ligand.itp\" 14L, 451C\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mError detected while processing command line:\u001b[m\r\r\n",
            "\u001b[1m\u001b[37m\u001b[41mE486: Pattern not found: 10     10     10\u001b[?2004l\u001b[m\r\r\n",
            "\"posre_ligand.itp\" 14L, 451C written\r\r\n",
            "\u001b[?2004l\u001b[?1l\u001b>\u001b[?25h\u001b[2J\u001b[?47l\u001b8turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K\n",
            "Calculated rlist for 1x1 atom pair-list as 1.010 nm, buffer size 0.010 nm\n",
            "Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm\n",
            "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
            "Calculating fourier grid dimensions for X Y Z\n",
            "Using a fourier grid of 64x64x64, spacing 0.153 0.153 0.155\n",
            "This run will generate roughly 30 Mb of data\n",
            "\u001b[?2004h\u001b7\u001b[?47h\u001b[?1h\u001b=\u001b[?2004h\u001b[1;24r\u001b[?12h\u001b[?12l\u001b[29m\u001b[m\u001b[H\u001b[2J\u001b[?25l\u001b[24;1H\"npt.mdp\" 47L, 2093C\u001b[?2004l\r\r\n",
            "\"npt.mdp\" 47L, 2094C written\r\r\n",
            "\u001b[?2004l\u001b[?1l\u001b>\u001b[?25h\u001b[2J\u001b[?47l\u001b8turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "turning all bonds into constraints...\n",
            "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K\n",
            "Calculated rlist for 1x1 atom pair-list as 1.010 nm, buffer size 0.010 nm\n",
            "Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm\n",
            "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
            "Calculating fourier grid dimensions for X Y Z\n",
            "Using a fourier grid of 64x64x64, spacing 0.153 0.153 0.154\n",
            "This run will generate roughly 30 Mb of data\n"
          ]
        },
        {
          "output_type": "stream",
          "name": "stderr",
          "text": [
            "Vim: Warning: Output is not to a terminal\n",
            "Vim: Warning: Input is not from a terminal\n",
            "Vim: Warning: Output is not to a terminal\n",
            "Vim: Warning: Input is not from a terminal\n",
            "Vim: Warning: Output is not to a terminal\n",
            "Vim: Warning: Input is not from a terminal\n",
            "                      :-) GROMACS - gmx grompp, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx grompp, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx grompp -f npt.mdp -c npt-1000.gro -t npt-1000.cpt -p topol.top -n index.ndx -o npt-100.tpr -r em.gro -maxwarn 2\n",
            "\n",
            "Ignoring obsolete mdp entry 'title'\n",
            "Ignoring obsolete mdp entry 'ns_type'\n",
            "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
            "\n",
            "NOTE 1 [file npt.mdp]:\n",
            "  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note\n",
            "  that with the Verlet scheme, nstlist has no effect on the accuracy of\n",
            "  your simulation.\n",
            "\n",
            "Setting the LD random seed to -269115803\n",
            "Generated 210 of the 2556 non-bonded parameter combinations\n",
            "Excluding 3 bonded neighbours molecule type 'Protein_chain_A'\n",
            "Excluding 3 bonded neighbours molecule type 'JZ4'\n",
            "Excluding 2 bonded neighbours molecule type 'SOL'\n",
            "Excluding 1 bonded neighbours molecule type 'NA'\n",
            "Excluding 1 bonded neighbours molecule type 'CL'\n",
            "\n",
            "WARNING 1 [file topol.top, line 11015]:\n",
            "  The GROMOS force fields have been parametrized with a physically\n",
            "  incorrect multiple-time-stepping scheme for a twin-range cut-off. When\n",
            "  used with a single-range cut-off (or a correct Trotter\n",
            "  multiple-time-stepping scheme), physical properties, such as the density,\n",
            "  might differ from the intended values. Since there are researchers\n",
            "  actively working on validating GROMOS with modern integrators we have not\n",
            "  yet removed the GROMOS force fields, but you should be aware of these\n",
            "  issues and check if molecules in your system are affected before\n",
            "  proceeding. Further information is available at\n",
            "  https://redmine.gromacs.org/issues/2884 , and a longer explanation of our\n",
            "  decision to remove physically incorrect algorithms can be found at\n",
            "  https://doi.org/10.26434/chemrxiv.11474583.v1 .\n",
            "\n",
            "Number of degrees of freedom in T-Coupling group Protein_JZ4 is 3389.95\n",
            "Number of degrees of freedom in T-Coupling group Water_and_ions is 184635.05\n",
            "Reading Coordinates, Velocities and Box size from old trajectory\n",
            "Will read whole trajectory\n",
            "\rLast frame         -1 time  100.000   \n",
            "Using frame at t = 100 ps\n",
            "Starting time for run is 0 ps\n",
            "Estimate for the relative computational load of the PME mesh part: 0.23\n",
            "\n",
            "There was 1 note\n",
            "\n",
            "There was 1 warning\n",
            "\n",
            "GROMACS reminds you: \"My Ass May Be Dumb, But I Ain't No Dumbass.\" (Jackie Brown)\n",
            "\n",
            "                      :-) GROMACS - gmx mdrun, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx mdrun, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx mdrun -deffnm npt-100 -v\n",
            "\n",
            "Reading file npt-100.tpr, VERSION 2020.6 (single precision)\n",
            "Changing nstlist from 5 to 80, rlist from 1 to 1.148\n",
            "\n",
            "1 GPU selected for this run.\n",
            "Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:\n",
            "  PP:0,PME:0\n",
            "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
            "PP task will update and constrain coordinates on the CPU\n",
            "PME tasks will do all aspects on the GPU\n",
            "Using 1 MPI thread\n",
            "\n",
            "Non-default thread affinity set, disabling internal thread affinity\n",
            "\n",
            "Using 2 OpenMP threads \n",
            "\n",
            "starting mdrun 'Protein in water'\n",
            "50000 steps,    100.0 ps.\n",
            "\rstep 0\rstep 100, remaining wall clock time:   255 s          \rstep 200, remaining wall clock time:   222 s          \rstep 300, remaining wall clock time:   206 s          \rstep 400, remaining wall clock time:   200 s          \rstep 500, remaining wall clock time:   194 s          \rstep 600, remaining wall clock time:   190 s          \rstep 700, remaining wall clock time:   186 s          \rstep 800, remaining wall clock time:   186 s          \rstep 900, remaining wall clock time:   183 s          \rstep 1000, remaining wall clock time:   181 s          \rstep 1100, remaining wall clock time:   180 s          \rstep 1200, remaining wall clock time:   180 s          \rstep 1300, remaining wall clock time:   178 s          \rstep 1400, remaining wall clock time:   183 s          \rstep 1520: timed with pme grid 64 64 64, coulomb cutoff 1.000: 604.4 M-cycles\n",
            "\rstep 1680: timed with pme grid 56 56 60, coulomb cutoff 1.087: 652.4 M-cycles\n",
            "\rstep 1840: timed with pme grid 52 52 52, coulomb cutoff 1.201: 763.2 M-cycles\n",
            "\rstep 2000: timed with pme grid 52 52 56, coulomb cutoff 1.170: 706.2 M-cycles\n",
            "\rstep 2160: timed with pme grid 56 56 56, coulomb cutoff 1.115: 651.0 M-cycles\n",
            "\rstep 2320: timed with pme grid 56 56 60, coulomb cutoff 1.087: 641.1 M-cycles\n",
            "\rstep 2480: timed with pme grid 60 60 60, coulomb cutoff 1.041: 634.5 M-cycles\n",
            "\rstep 2640: timed with pme grid 60 60 64, coulomb cutoff 1.014: 630.7 M-cycles\n",
            "\rstep 2800: timed with pme grid 64 64 64, coulomb cutoff 1.000: 635.8 M-cycles\n",
            "\r              optimal pme grid 64 64 64, coulomb cutoff 1.000\n",
            "\rstep 2900, remaining wall clock time:   235 s          \rstep 3000, remaining wall clock time:   232 s          \rstep 3100, remaining wall clock time:   229 s          \rstep 3200, remaining wall clock time:   227 s          \rstep 3300, remaining wall clock time:   224 s          \rstep 3400, remaining wall clock time:   222 s          \rstep 3500, remaining wall clock time:   220 s          \rstep 3600, remaining wall clock time:   218 s          \rstep 3700, remaining wall clock time:   216 s          \rstep 3800, remaining wall clock time:   214 s          \rstep 3900, remaining wall clock time:   212 s          \rstep 4000, remaining wall clock time:   211 s          \rstep 4100, remaining wall clock time:   209 s          \rstep 4200, remaining wall clock time:   207 s          \rstep 4300, remaining wall clock time:   206 s          \rstep 4400, remaining wall clock time:   204 s          \rstep 4500, remaining wall clock time:   203 s          \rstep 4600, remaining wall clock time:   201 s          \rstep 4700, remaining wall clock time:   200 s          \rstep 4800, remaining wall clock time:   199 s          \rstep 4900, remaining wall clock time:   198 s          \rstep 5000, remaining wall clock time:   197 s          \rstep 5100, remaining wall clock time:   195 s          \rstep 5200, remaining wall clock time:   195 s          \rstep 5300, remaining wall clock time:   193 s          \rstep 5400, remaining wall clock time:   192 s          \rstep 5500, remaining wall clock time:   191 s          \rstep 5600, remaining wall clock time:   190 s          \rstep 5700, remaining wall clock time:   189 s          \rstep 5800, remaining wall clock time:   188 s          \rstep 5900, remaining wall clock time:   187 s          \rstep 6000, remaining wall clock time:   186 s          \rstep 6100, remaining wall clock time:   185 s          \rstep 6200, remaining wall clock time:   184 s          \rstep 6300, remaining wall clock time:   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            "Writing final coordinates.\n",
            "\rstep 50000, remaining wall clock time:     0 s          \n",
            "NOTE: 12 % of the run time was spent in pair search,\n",
            "      you might want to increase nstlist (this has no effect on accuracy)\n",
            "\n",
            "               Core t (s)   Wall t (s)        (%)\n",
            "       Time:      367.962      183.981      200.0\n",
            "                 (ns/day)    (hour/ns)\n",
            "Performance:       46.962        0.511\n",
            "\n",
            "GROMACS reminds you: \"Everything's formed from particles\" (Van der Graaf Generator)\n",
            "\n",
            "Vim: Warning: Output is not to a terminal\n",
            "Vim: Warning: Input is not from a terminal\n",
            "Vim: Warning: Output is not to a terminal\n",
            "Vim: Warning: Input is not from a terminal\n",
            "Vim: Warning: Output is not to a terminal\n",
            "Vim: Warning: Input is not from a terminal\n",
            "                      :-) GROMACS - gmx grompp, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx grompp, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx grompp -f npt.mdp -c npt-100.gro -t npt-100.cpt -p topol.top -n index.ndx -o npt-10.tpr -r em.gro -maxwarn 2\n",
            "\n",
            "Ignoring obsolete mdp entry 'title'\n",
            "Ignoring obsolete mdp entry 'ns_type'\n",
            "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
            "\n",
            "NOTE 1 [file npt.mdp]:\n",
            "  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note\n",
            "  that with the Verlet scheme, nstlist has no effect on the accuracy of\n",
            "  your simulation.\n",
            "\n",
            "Setting the LD random seed to -270651485\n",
            "Generated 210 of the 2556 non-bonded parameter combinations\n",
            "Excluding 3 bonded neighbours molecule type 'Protein_chain_A'\n",
            "Excluding 3 bonded neighbours molecule type 'JZ4'\n",
            "Excluding 2 bonded neighbours molecule type 'SOL'\n",
            "Excluding 1 bonded neighbours molecule type 'NA'\n",
            "Excluding 1 bonded neighbours molecule type 'CL'\n",
            "\n",
            "WARNING 1 [file topol.top, line 11015]:\n",
            "  The GROMOS force fields have been parametrized with a physically\n",
            "  incorrect multiple-time-stepping scheme for a twin-range cut-off. When\n",
            "  used with a single-range cut-off (or a correct Trotter\n",
            "  multiple-time-stepping scheme), physical properties, such as the density,\n",
            "  might differ from the intended values. Since there are researchers\n",
            "  actively working on validating GROMOS with modern integrators we have not\n",
            "  yet removed the GROMOS force fields, but you should be aware of these\n",
            "  issues and check if molecules in your system are affected before\n",
            "  proceeding. Further information is available at\n",
            "  https://redmine.gromacs.org/issues/2884 , and a longer explanation of our\n",
            "  decision to remove physically incorrect algorithms can be found at\n",
            "  https://doi.org/10.26434/chemrxiv.11474583.v1 .\n",
            "\n",
            "Number of degrees of freedom in T-Coupling group Protein_JZ4 is 3389.95\n",
            "Number of degrees of freedom in T-Coupling group Water_and_ions is 184635.05\n",
            "Reading Coordinates, Velocities and Box size from old trajectory\n",
            "Will read whole trajectory\n",
            "\rLast frame         -1 time  100.000   \n",
            "Using frame at t = 100 ps\n",
            "Starting time for run is 0 ps\n",
            "Estimate for the relative computational load of the PME mesh part: 0.23\n",
            "\n",
            "There was 1 note\n",
            "\n",
            "There was 1 warning\n",
            "\n",
            "GROMACS reminds you: \"As Always Your Logic Is Impeccable\" (Tuvok)\n",
            "\n",
            "                      :-) GROMACS - gmx mdrun, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx mdrun, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx mdrun -deffnm npt-10 -v\n",
            "\n",
            "Reading file npt-10.tpr, VERSION 2020.6 (single precision)\n",
            "Changing nstlist from 5 to 80, rlist from 1 to 1.148\n",
            "\n",
            "1 GPU selected for this run.\n",
            "Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:\n",
            "  PP:0,PME:0\n",
            "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
            "PP task will update and constrain coordinates on the CPU\n",
            "PME tasks will do all aspects on the GPU\n",
            "Using 1 MPI thread\n",
            "\n",
            "Non-default thread affinity set, disabling internal thread affinity\n",
            "\n",
            "Using 2 OpenMP threads \n",
            "\n",
            "starting mdrun 'Protein in water'\n",
            "50000 steps,    100.0 ps.\n",
            "\rstep 0\rstep 100, remaining wall clock time:   260 s          \rstep 200, remaining wall clock time:   225 s          \rstep 300, remaining wall clock time:   214 s          \rstep 400, remaining wall clock time:   211 s          \rstep 500, remaining wall clock time:   203 s          \rstep 600, remaining wall clock time:   197 s          \rstep 700, remaining wall clock time:   194 s          \rstep 800, remaining wall clock time:   193 s          \rstep 900, remaining wall clock time:   192 s          \rstep 1000, remaining wall clock time:   189 s          \rstep 1100, remaining wall clock time:   187 s          \rstep 1200, remaining wall clock time:   187 s          \rstep 1300, remaining wall clock time:   185 s          \rstep 1440: timed with pme grid 64 64 64, coulomb cutoff 1.000: 643.0 M-cycles\n",
            "\rstep 1600: timed with pme grid 56 56 56, coulomb cutoff 1.099: 701.9 M-cycles\n",
            "\rstep 1760: timed with pme grid 48 48 48, coulomb cutoff 1.283: 768.3 M-cycles\n",
            "\rstep 1920: timed with pme grid 52 52 48, coulomb cutoff 1.277: 779.0 M-cycles\n",
            "\rstep 2080: timed with pme grid 52 52 52, coulomb cutoff 1.184: 734.3 M-cycles\n",
            "\rstep 2240: timed with pme grid 56 56 56, coulomb cutoff 1.099: 671.3 M-cycles\n",
            "\rstep 2400: timed with pme grid 60 60 60, coulomb cutoff 1.026: 683.1 M-cycles\n",
            "\rstep 2560: timed with pme grid 64 64 64, coulomb cutoff 1.000: 625.5 M-cycles\n",
            "\rstep 2720: timed with pme grid 56 56 56, coulomb cutoff 1.099: 658.9 M-cycles\n",
            "\rstep 2880: timed with pme grid 60 60 60, coulomb cutoff 1.026: 648.9 M-cycles\n",
            "\rstep 3040: timed with pme grid 64 64 64, coulomb cutoff 1.000: 648.5 M-cycles\n",
            "\rstep 3200: timed with pme grid 56 56 56, coulomb cutoff 1.099: 714.8 M-cycles\n",
            "\rstep 3360: timed with pme grid 60 60 60, coulomb cutoff 1.026: 650.8 M-cycles\n",
            "\rstep 3520: timed with pme grid 64 64 64, coulomb cutoff 1.000: 619.0 M-cycles\n",
            "\r              optimal pme grid 64 64 64, coulomb cutoff 1.000\n",
            "\rstep 3600, remaining wall clock time:   224 s          \rstep 3700, remaining wall clock time:   221 s          \rstep 3800, remaining wall clock time:   219 s          \rstep 3900, remaining wall clock time:   217 s          \rstep 4000, remaining wall clock time:   216 s          \rstep 4100, remaining wall clock time:   214 s          \rstep 4200, remaining wall clock time:   212 s          \rstep 4300, remaining wall clock time:   211 s          \rstep 4400, remaining wall clock time:   209 s          \rstep 4500, remaining wall clock time:   208 s          \rstep 4600, remaining wall clock time:   206 s          \rstep 4700, remaining wall clock time:   205 s          \rstep 4800, remaining wall clock time:   204 s          \rstep 4900, remaining wall clock time:   202 s          \rstep 5000, remaining wall clock time:   201 s          \rstep 5100, remaining wall clock time:   200 s          \rstep 5200, remaining wall clock time:   199 s          \rstep 5300, 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\rstep 48500, remaining wall clock time:     5 s          \rstep 48600, remaining wall clock time:     5 s          \rstep 48700, remaining wall clock time:     4 s          \rstep 48800, remaining wall clock time:     4 s          \rstep 48900, remaining wall clock time:     4 s          \rstep 49000, remaining wall clock time:     3 s          \rstep 49100, remaining wall clock time:     3 s          \rstep 49200, remaining wall clock time:     2 s          \rstep 49300, remaining wall clock time:     2 s          \rstep 49400, remaining wall clock time:     2 s          \rstep 49500, remaining wall clock time:     1 s          \rstep 49600, remaining wall clock time:     1 s          \rstep 49700, remaining wall clock time:     1 s          \rstep 49800, remaining wall clock time:     0 s          \rstep 49900, remaining wall clock time:     0 s          \n",
            "Writing final coordinates.\n",
            "\rstep 50000, remaining wall clock time:     0 s          \n",
            "NOTE: 12 % of the run time was spent in pair search,\n",
            "      you might want to increase nstlist (this has no effect on accuracy)\n",
            "\n",
            "               Core t (s)   Wall t (s)        (%)\n",
            "       Time:      369.700      184.851      200.0\n",
            "                 (ns/day)    (hour/ns)\n",
            "Performance:       46.741        0.513\n",
            "\n",
            "GROMACS reminds you: \"Science and everyday life cannot and should not be separated.\" (Rosalind Franklin)\n",
            "\n",
            "Vim: Warning: Output is not to a terminal\n",
            "Vim: Warning: Input is not from a terminal\n",
            "Vim: Warning: Output is not to a terminal\n",
            "Vim: Warning: Input is not from a terminal\n",
            "Vim: Warning: Output is not to a terminal\n",
            "Vim: Warning: Input is not from a terminal\n",
            "                      :-) GROMACS - gmx grompp, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx grompp, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx grompp -f npt.mdp -c npt-10.gro -t npt-10.cpt -p topol.top -n index.ndx -o npt-1.tpr -r em.gro -maxwarn 2\n",
            "\n",
            "Ignoring obsolete mdp entry 'title'\n",
            "Ignoring obsolete mdp entry 'ns_type'\n",
            "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
            "\n",
            "NOTE 1 [file npt.mdp]:\n",
            "  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note\n",
            "  that with the Verlet scheme, nstlist has no effect on the accuracy of\n",
            "  your simulation.\n",
            "\n",
            "Setting the LD random seed to -403048657\n",
            "Generated 210 of the 2556 non-bonded parameter combinations\n",
            "Excluding 3 bonded neighbours molecule type 'Protein_chain_A'\n",
            "Excluding 3 bonded neighbours molecule type 'JZ4'\n",
            "Excluding 2 bonded neighbours molecule type 'SOL'\n",
            "Excluding 1 bonded neighbours molecule type 'NA'\n",
            "Excluding 1 bonded neighbours molecule type 'CL'\n",
            "\n",
            "WARNING 1 [file topol.top, line 11015]:\n",
            "  The GROMOS force fields have been parametrized with a physically\n",
            "  incorrect multiple-time-stepping scheme for a twin-range cut-off. When\n",
            "  used with a single-range cut-off (or a correct Trotter\n",
            "  multiple-time-stepping scheme), physical properties, such as the density,\n",
            "  might differ from the intended values. Since there are researchers\n",
            "  actively working on validating GROMOS with modern integrators we have not\n",
            "  yet removed the GROMOS force fields, but you should be aware of these\n",
            "  issues and check if molecules in your system are affected before\n",
            "  proceeding. Further information is available at\n",
            "  https://redmine.gromacs.org/issues/2884 , and a longer explanation of our\n",
            "  decision to remove physically incorrect algorithms can be found at\n",
            "  https://doi.org/10.26434/chemrxiv.11474583.v1 .\n",
            "\n",
            "Number of degrees of freedom in T-Coupling group Protein_JZ4 is 3389.95\n",
            "Number of degrees of freedom in T-Coupling group Water_and_ions is 184635.05\n",
            "Reading Coordinates, Velocities and Box size from old trajectory\n",
            "Will read whole trajectory\n",
            "\rLast frame         -1 time  100.000   \n",
            "Using frame at t = 100 ps\n",
            "Starting time for run is 0 ps\n",
            "Estimate for the relative computational load of the PME mesh part: 0.23\n",
            "\n",
            "There was 1 note\n",
            "\n",
            "There was 1 warning\n",
            "\n",
            "GROMACS reminds you: \"It's Not Dark Yet, But It's Getting There\" (Bob Dylan)\n",
            "\n",
            "                      :-) GROMACS - gmx mdrun, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx mdrun, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx mdrun -deffnm npt-1 -v\n",
            "\n",
            "Reading file npt-1.tpr, VERSION 2020.6 (single precision)\n",
            "Changing nstlist from 5 to 80, rlist from 1 to 1.148\n",
            "\n",
            "1 GPU selected for this run.\n",
            "Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:\n",
            "  PP:0,PME:0\n",
            "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
            "PP task will update and constrain coordinates on the CPU\n",
            "PME tasks will do all aspects on the GPU\n",
            "Using 1 MPI thread\n",
            "\n",
            "Non-default thread affinity set, disabling internal thread affinity\n",
            "\n",
            "Using 2 OpenMP threads \n",
            "\n",
            "starting mdrun 'Protein in water'\n",
            "50000 steps,    100.0 ps.\n",
            "\rstep 0\rstep 100, remaining wall clock time:   257 s          \rstep 200, remaining wall clock time:   222 s          \rstep 300, remaining wall clock time:   214 s          \rstep 400, remaining wall clock time:   208 s          \rstep 500, remaining wall clock time:   200 s          \rstep 600, remaining wall clock time:   196 s          \rstep 700, remaining wall clock time:   191 s          \rstep 800, remaining wall clock time:   190 s          \rstep 900, remaining wall clock time:   188 s          \rstep 1000, remaining wall clock time:   185 s          \rstep 1100, remaining wall clock time:   183 s          \rstep 1200, remaining wall clock time:   184 s          \rstep 1300, remaining wall clock time:   182 s          \rstep 1440: timed with pme grid 64 64 64, coulomb cutoff 1.000: 646.1 M-cycles\n",
            "\rstep 1600: timed with pme grid 56 56 60, coulomb cutoff 1.094: 659.4 M-cycles\n",
            "\rstep 1760: timed with pme grid 52 52 52, coulomb cutoff 1.190: 738.2 M-cycles\n",
            "\rstep 1920: timed with pme grid 52 52 56, coulomb cutoff 1.178: 708.2 M-cycles\n",
            "\rstep 2080: timed with pme grid 56 56 56, coulomb cutoff 1.105: 677.2 M-cycles\n",
            "\rstep 2240: timed with pme grid 56 56 60, coulomb cutoff 1.094: 682.3 M-cycles\n",
            "\rstep 2400: timed with pme grid 60 60 60, coulomb cutoff 1.031: 625.5 M-cycles\n",
            "\rstep 2560: timed with pme grid 60 60 64, coulomb cutoff 1.021: 627.1 M-cycles\n",
            "\rstep 2720: timed with pme grid 64 64 64, coulomb cutoff 1.000: 615.0 M-cycles\n",
            "\rstep 2880: timed with pme grid 56 56 56, coulomb cutoff 1.105: 663.1 M-cycles\n",
            "\rstep 3040: timed with pme grid 56 56 60, coulomb cutoff 1.094: 684.3 M-cycles\n",
            "\rstep 3200: timed with pme grid 60 60 60, coulomb cutoff 1.031: 653.9 M-cycles\n",
            "\rstep 3360: timed with pme grid 60 60 64, coulomb cutoff 1.021: 630.9 M-cycles\n",
            "\rstep 3520: timed with pme grid 64 64 64, coulomb cutoff 1.000: 637.9 M-cycles\n",
            "\rstep 3680: timed with pme grid 56 56 56, coulomb cutoff 1.105: 674.9 M-cycles\n",
            "\rstep 3840: timed with pme grid 56 56 60, coulomb cutoff 1.094: 663.1 M-cycles\n",
            "\rstep 4000: timed with pme grid 60 60 60, coulomb cutoff 1.031: 662.5 M-cycles\n",
            "\rstep 4160: timed with pme grid 60 60 64, coulomb cutoff 1.021: 637.6 M-cycles\n",
            "\rstep 4320: timed with pme grid 64 64 64, coulomb cutoff 1.000: 653.8 M-cycles\n",
            "\r              optimal pme grid 64 64 64, coulomb cutoff 1.000\n",
            "\rstep 4400, remaining wall clock time:   208 s          \rstep 4500, remaining wall clock time:   206 s          \rstep 4600, remaining wall clock time:   205 s          \rstep 4700, remaining wall clock time:   203 s          \rstep 4800, remaining wall clock time:   202 s          \rstep 4900, remaining wall clock time:   201 s          \rstep 5000, remaining wall clock time:   200 s          \rstep 5100, remaining wall clock time:   198 s          \rstep 5200, remaining wall clock time:   198 s          \rstep 5300, remaining wall clock time:   196 s          \rstep 5400, remaining wall clock time:   195 s          \rstep 5500, remaining wall clock time:   194 s          \rstep 5600, remaining wall clock time:   193 s          \rstep 5700, remaining wall clock time:   192 s          \rstep 5800, remaining wall clock time:   191 s          \rstep 5900, remaining wall clock time:   190 s          \rstep 6000, remaining wall clock time:   189 s          \rstep 6100, remaining wall clock time:   188 s          \rstep 6200, remaining wall clock time:   187 s          \rstep 6300, remaining wall clock time:   186 s          \rstep 6400, remaining wall clock time:   185 s          \rstep 6500, remaining wall clock time:   184 s          \rstep 6600, remaining wall clock time:   184 s          \rstep 6700, remaining wall clock time:   183 s          \rstep 6800, remaining wall clock time:   182 s          \rstep 6900, remaining wall clock time:   181 s          \rstep 7000, remaining wall clock time:   180 s          \rstep 7100, remaining wall clock time:   179 s          \rstep 7200, remaining wall clock time:   179 s          \rstep 7300, remaining wall clock time:   178 s          \rstep 7400, remaining wall clock time:   177 s          \rstep 7500, remaining wall clock time:   176 s          \rstep 7600, remaining wall clock time:   175 s          \rstep 7700, remaining wall clock time:   175 s          \rstep 7800, remaining wall clock time:   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remaining wall clock time:   163 s          \rstep 9700, remaining wall clock time:   162 s          \rstep 9800, remaining wall clock time:   161 s          \rstep 9900, remaining wall clock time:   161 s          \rstep 10000, remaining wall clock time:   160 s          \rstep 10100, remaining wall clock time:   160 s          \rstep 10200, remaining wall clock time:   159 s          \rstep 10300, remaining wall clock time:   159 s          \rstep 10400, remaining wall clock time:   158 s          \rstep 10500, remaining wall clock time:   157 s          \rstep 10600, remaining wall clock time:   157 s          \rstep 10700, remaining wall clock time:   156 s          \rstep 10800, remaining wall clock time:   156 s          \rstep 10900, remaining wall clock time:   155 s          \rstep 11000, remaining wall clock time:   155 s          \rstep 11100, remaining wall clock time:   154 s          \rstep 11200, remaining wall clock time:   154 s          \rstep 11300, remaining wall 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            "Writing final coordinates.\n",
            "\rstep 50000, remaining wall clock time:     0 s          \n",
            "NOTE: 12 % of the run time was spent in pair search,\n",
            "      you might want to increase nstlist (this has no effect on accuracy)\n",
            "\n",
            "               Core t (s)   Wall t (s)        (%)\n",
            "       Time:      365.174      182.587      200.0\n",
            "                 (ns/day)    (hour/ns)\n",
            "Performance:       47.321        0.507\n",
            "\n",
            "GROMACS reminds you: \"It is now quite lawful for a Catholic woman to avoid pregnancy by a resort to mathematics, though she is still forbidden to resort to physics and chemistry.\" (Henry Louis Mencken)\n",
            "\n",
            "Vim: Warning: Output is not to a terminal\n",
            "Vim: Warning: Input is not from a terminal\n",
            "                      :-) GROMACS - gmx grompp, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx grompp, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx grompp -f npt.mdp -c npt-1.gro -t npt-1.cpt -p topol.top -n index.ndx -o npt.tpr -r em.gro -maxwarn 2\n",
            "\n",
            "Ignoring obsolete mdp entry 'title'\n",
            "Ignoring obsolete mdp entry 'ns_type'\n",
            "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
            "\n",
            "NOTE 1 [file npt.mdp]:\n",
            "  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note\n",
            "  that with the Verlet scheme, nstlist has no effect on the accuracy of\n",
            "  your simulation.\n",
            "\n",
            "Setting the LD random seed to 2046738174\n",
            "Generated 210 of the 2556 non-bonded parameter combinations\n",
            "Excluding 3 bonded neighbours molecule type 'Protein_chain_A'\n",
            "Excluding 3 bonded neighbours molecule type 'JZ4'\n",
            "Excluding 2 bonded neighbours molecule type 'SOL'\n",
            "Excluding 1 bonded neighbours molecule type 'NA'\n",
            "Excluding 1 bonded neighbours molecule type 'CL'\n",
            "\n",
            "WARNING 1 [file topol.top, line 11015]:\n",
            "  The GROMOS force fields have been parametrized with a physically\n",
            "  incorrect multiple-time-stepping scheme for a twin-range cut-off. When\n",
            "  used with a single-range cut-off (or a correct Trotter\n",
            "  multiple-time-stepping scheme), physical properties, such as the density,\n",
            "  might differ from the intended values. Since there are researchers\n",
            "  actively working on validating GROMOS with modern integrators we have not\n",
            "  yet removed the GROMOS force fields, but you should be aware of these\n",
            "  issues and check if molecules in your system are affected before\n",
            "  proceeding. Further information is available at\n",
            "  https://redmine.gromacs.org/issues/2884 , and a longer explanation of our\n",
            "  decision to remove physically incorrect algorithms can be found at\n",
            "  https://doi.org/10.26434/chemrxiv.11474583.v1 .\n",
            "\n",
            "Number of degrees of freedom in T-Coupling group Protein_JZ4 is 3389.95\n",
            "Number of degrees of freedom in T-Coupling group Water_and_ions is 184635.05\n",
            "Reading Coordinates, Velocities and Box size from old trajectory\n",
            "Will read whole trajectory\n",
            "\rLast frame         -1 time  100.000   \n",
            "Using frame at t = 100 ps\n",
            "Starting time for run is 0 ps\n",
            "Estimate for the relative computational load of the PME mesh part: 0.23\n",
            "\n",
            "There was 1 note\n",
            "\n",
            "There was 1 warning\n",
            "\n",
            "GROMACS reminds you: \"When my information changes, I alter my conclusions. What do you do, sir?\" (John Maynard Keynes)\n",
            "\n",
            "                      :-) GROMACS - gmx mdrun, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx mdrun, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx mdrun -deffnm npt -v\n",
            "\n",
            "Reading file npt.tpr, VERSION 2020.6 (single precision)\n",
            "Changing nstlist from 5 to 80, rlist from 1 to 1.148\n",
            "\n",
            "1 GPU selected for this run.\n",
            "Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:\n",
            "  PP:0,PME:0\n",
            "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
            "PP task will update and constrain coordinates on the CPU\n",
            "PME tasks will do all aspects on the GPU\n",
            "Using 1 MPI thread\n",
            "\n",
            "Non-default thread affinity set, disabling internal thread affinity\n",
            "\n",
            "Using 2 OpenMP threads \n",
            "\n",
            "starting mdrun 'Protein in water'\n",
            "50000 steps,    100.0 ps.\n",
            "\rstep 0\rstep 100, remaining wall clock time:   260 s          \rstep 200, remaining wall clock time:   222 s          \rstep 300, remaining wall clock time:   206 s          \rstep 400, remaining wall clock time:   203 s          \rstep 500, remaining wall clock time:   196 s          \rstep 600, remaining wall clock time:   191 s          \rstep 700, remaining wall clock time:   188 s          \rstep 800, remaining wall clock time:   187 s          \rstep 900, remaining wall clock time:   186 s          \rstep 1000, remaining wall clock time:   183 s          \rstep 1100, remaining wall clock time:   181 s          \rstep 1200, remaining wall clock time:   182 s          \rstep 1300, remaining wall clock time:   181 s          \rstep 1440: timed with pme grid 64 64 64, coulomb cutoff 1.000: 618.4 M-cycles\n",
            "\rstep 1600: timed with pme grid 56 56 56, coulomb cutoff 1.103: 655.8 M-cycles\n",
            "\rstep 1760: timed with pme grid 48 48 48, coulomb cutoff 1.287: 753.4 M-cycles\n",
            "\rstep 1920: timed with pme grid 48 48 52, coulomb cutoff 1.277: 748.7 M-cycles\n",
            "\rstep 2080: timed with pme grid 52 52 52, coulomb cutoff 1.188: 732.1 M-cycles\n",
            "\rstep 2240: timed with pme grid 52 52 56, coulomb cutoff 1.178: 724.3 M-cycles\n",
            "\rstep 2400: timed with pme grid 56 56 56, coulomb cutoff 1.103: 655.3 M-cycles\n",
            "\rstep 2560: timed with pme grid 60 60 60, coulomb cutoff 1.029: 615.6 M-cycles\n",
            "\rstep 2720: timed with pme grid 60 60 64, coulomb cutoff 1.021: 645.5 M-cycles\n",
            "\rstep 2880: timed with pme grid 64 64 64, coulomb cutoff 1.000: 626.1 M-cycles\n",
            "\r              optimal pme grid 60 60 60, coulomb cutoff 1.029\n",
            "\rstep 3000, remaining wall clock time:   242 s          \rstep 3100, remaining wall clock time:   239 s          \rstep 3200, remaining wall clock time:   237 s          \rstep 3300, remaining wall clock time:   234 s          \rstep 3400, remaining wall clock time:   232 s          \rstep 3500, remaining wall clock time:   229 s          \rstep 3600, remaining wall clock time:   228 s          \rstep 3700, remaining wall clock time:   225 s          \rstep 3800, remaining wall clock time:   223 s          \rstep 3900, remaining wall clock time:   221 s          \rstep 4000, remaining wall clock time:   220 s          \rstep 4100, remaining wall clock time:   218 s          \rstep 4200, remaining wall clock time:   216 s          \rstep 4300, remaining wall clock time:   214 s          \rstep 4400, remaining wall clock time:   213 s          \rstep 4500, remaining wall clock time:   211 s          \rstep 4600, remaining wall clock time:   210 s          \rstep 4700, 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remaining wall clock time:     7 s          \rstep 48000, remaining wall clock time:     7 s          \rstep 48100, remaining wall clock time:     7 s          \rstep 48200, remaining wall clock time:     6 s          \rstep 48300, remaining wall clock time:     6 s          \rstep 48400, remaining wall clock time:     6 s          \rstep 48500, remaining wall clock time:     5 s          \rstep 48600, remaining wall clock time:     5 s          \rstep 48700, remaining wall clock time:     4 s          \rstep 48800, remaining wall clock time:     4 s          \rstep 48900, remaining wall clock time:     4 s          \rstep 49000, remaining wall clock time:     3 s          \rstep 49100, remaining wall clock time:     3 s          \rstep 49200, remaining wall clock time:     3 s          \rstep 49300, remaining wall clock time:     2 s          \rstep 49400, remaining wall clock time:     2 s          \rstep 49500, remaining wall clock time:     1 s          \rstep 49600, remaining wall clock time:     1 s          \rstep 49700, remaining wall clock time:     1 s          \rstep 49800, remaining wall clock time:     0 s          \rstep 49900, remaining wall clock time:     0 s          \n",
            "Writing final coordinates.\n",
            "\rstep 50000, remaining wall clock time:     0 s          \n",
            "NOTE: 12 % of the run time was spent in pair search,\n",
            "      you might want to increase nstlist (this has no effect on accuracy)\n",
            "\n",
            "               Core t (s)   Wall t (s)        (%)\n",
            "       Time:      377.516      188.758      200.0\n",
            "                 (ns/day)    (hour/ns)\n",
            "Performance:       45.774        0.524\n",
            "\n",
            "GROMACS reminds you: \"Research ! A mere excuse for idleness; it has never achieved, and will never achieve any results of the slightest value.\" (Benjamin Jowett, British theologian, 1817-93)\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!/content/gromacs/bin/gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o protein-ligand-out.tpr -maxwarn 2\n",
        "!/content/gromacs/bin/gmx mdrun -deffnm protein-ligand-out -v\n"
      ],
      "metadata": {
        "id": "bkvz9YmcBv2j",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "1aba2cd7-2632-4f68-fe4d-bed61625f027"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "                      :-) GROMACS - gmx grompp, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx grompp, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o protein-ligand-out.tpr -maxwarn 2\n",
            "\n",
            "Ignoring obsolete mdp entry 'title'\n",
            "Ignoring obsolete mdp entry 'ns_type'\n",
            "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
            "\n",
            "NOTE 1 [file md.mdp]:\n",
            "  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note\n",
            "  that with the Verlet scheme, nstlist has no effect on the accuracy of\n",
            "  your simulation.\n",
            "\n",
            "Setting the LD random seed to -671227453\n",
            "Generated 210 of the 2556 non-bonded parameter combinations\n",
            "Excluding 3 bonded neighbours molecule type 'Protein_chain_A'\n",
            "turning all bonds into constraints...\n",
            "Excluding 3 bonded neighbours molecule type 'JZ4'\n",
            "turning all bonds into constraints...\n",
            "Excluding 2 bonded neighbours molecule type 'SOL'\n",
            "turning all bonds into constraints...\n",
            "Excluding 1 bonded neighbours molecule type 'NA'\n",
            "turning all bonds into constraints...\n",
            "Excluding 1 bonded neighbours molecule type 'CL'\n",
            "turning all bonds into constraints...\n",
            "\n",
            "WARNING 1 [file topol.top, line 11015]:\n",
            "  The GROMOS force fields have been parametrized with a physically\n",
            "  incorrect multiple-time-stepping scheme for a twin-range cut-off. When\n",
            "  used with a single-range cut-off (or a correct Trotter\n",
            "  multiple-time-stepping scheme), physical properties, such as the density,\n",
            "  might differ from the intended values. Since there are researchers\n",
            "  actively working on validating GROMOS with modern integrators we have not\n",
            "  yet removed the GROMOS force fields, but you should be aware of these\n",
            "  issues and check if molecules in your system are affected before\n",
            "  proceeding. Further information is available at\n",
            "  https://redmine.gromacs.org/issues/2884 , and a longer explanation of our\n",
            "  decision to remove physically incorrect algorithms can be found at\n",
            "  https://doi.org/10.26434/chemrxiv.11474583.v1 .\n",
            "\n",
            "Number of degrees of freedom in T-Coupling group Protein_JZ4 is 3389.95\n",
            "Number of degrees of freedom in T-Coupling group Water_and_ions is 184635.05\n",
            "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K\n",
            "Calculated rlist for 1x1 atom pair-list as 1.010 nm, buffer size 0.010 nm\n",
            "Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm\n",
            "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
            "Reading Coordinates, Velocities and Box size from old trajectory\n",
            "Will read whole trajectory\n",
            "Last frame         -1 time  100.000   \n",
            "Using frame at t = 100 ps\n",
            "Starting time for run is 0 ps\n",
            "Calculating fourier grid dimensions for X Y Z\n",
            "Using a fourier grid of 64x64x64, spacing 0.154 0.154 0.153\n",
            "Estimate for the relative computational load of the PME mesh part: 0.23\n",
            "This run will generate roughly 17 Mb of data\n",
            "\n",
            "There was 1 note\n",
            "\n",
            "There was 1 warning\n",
            "\n",
            "GROMACS reminds you: \"An intellectual is someone who has found something more interesting than sex.\" (Edgar Wallace)\n",
            "\n",
            "                      :-) GROMACS - gmx mdrun, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx mdrun, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx mdrun -deffnm protein-ligand-out -v\n",
            "\n",
            "Reading file protein-ligand-out.tpr, VERSION 2020.6 (single precision)\n",
            "Changing nstlist from 5 to 80, rlist from 1 to 1.148\n",
            "\n",
            "1 GPU selected for this run.\n",
            "Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:\n",
            "  PP:0,PME:0\n",
            "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
            "PP task will update and constrain coordinates on the CPU\n",
            "PME tasks will do all aspects on the GPU\n",
            "Using 1 MPI thread\n",
            "\n",
            "Non-default thread affinity set, disabling internal thread affinity\n",
            "\n",
            "Using 2 OpenMP threads \n",
            "\n",
            "starting mdrun 'Protein in water'\n",
            "100000 steps,    200.0 ps.\n",
            "step 1440: timed with pme grid 64 64 64, coulomb cutoff 1.000: 624.8 M-cycles\n",
            "step 1600: timed with pme grid 56 56 56, coulomb cutoff 1.098: 644.2 M-cycles\n",
            "step 1760: timed with pme grid 48 48 48, coulomb cutoff 1.281: 756.5 M-cycles\n",
            "step 1920: timed with pme grid 52 52 48, coulomb cutoff 1.275: 797.9 M-cycles\n",
            "step 2080: timed with pme grid 52 52 52, coulomb cutoff 1.183: 777.7 M-cycles\n",
            "step 2240: timed with pme grid 56 56 52, coulomb cutoff 1.177: 706.6 M-cycles\n",
            "step 2400: timed with pme grid 56 56 56, coulomb cutoff 1.098: 660.4 M-cycles\n",
            "step 2560: timed with pme grid 60 60 60, coulomb cutoff 1.025: 623.1 M-cycles\n",
            "step 2720: timed with pme grid 64 64 64, coulomb cutoff 1.000: 611.9 M-cycles\n",
            "step 2880: timed with pme grid 56 56 56, coulomb cutoff 1.098: 658.4 M-cycles\n",
            "step 3040: timed with pme grid 60 60 60, coulomb cutoff 1.025: 635.2 M-cycles\n",
            "step 3200: timed with pme grid 64 64 64, coulomb cutoff 1.000: 645.0 M-cycles\n",
            "              optimal pme grid 64 64 64, coulomb cutoff 1.000\n",
            "step 99900, remaining wall clock time:     0 s          \n",
            "Writing final coordinates.\n",
            "step 100000, remaining wall clock time:     0 s          \n",
            "NOTE: 12 % of the run time was spent in pair search,\n",
            "      you might want to increase nstlist (this has no effect on accuracy)\n",
            "\n",
            "               Core t (s)   Wall t (s)        (%)\n",
            "       Time:      742.540      371.270      200.0\n",
            "                 (ns/day)    (hour/ns)\n",
            "Performance:       46.543        0.516\n",
            "\n",
            "GROMACS reminds you: \"What Kind Of Guru are You, Anyway ?\" (F. Zappa)\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#@title Analysis\n",
        "%%bash\n",
        "source /content/gromacs/bin/GMXRC\n",
        "printf '1\\n1' | gmx trjconv -s protein-ligand-out.tpr -f protein-ligand-out.xtc -o protein-ligand-out.pdb -pbc cluster\n",
        "printf '1\\n1' | gmx trjconv -s protein-ligand-out.tpr -f protein-ligand-out.xtc -o protein-0-10ns.xtc -pbc cluster\n",
        "printf '4\\n4' | gmx rms -s protein-ligand-out.tpr -f protein-ligand-out.pdb -o protein-0-1-RMSD.xvg \n",
        "gmx rmsf -s protein-ligand-out.tpr -f protein-ligand-out.pdb -o protein-0-10ns-RMSF.xvg -res <<< 3"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "WUF1CsSUwZem",
        "outputId": "44bea9bf-ae32-46b2-daeb-a174b75443fa"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Note that major changes are planned in future for trjconv, to improve usability and utility.\n",
            "Select group for clustering\n",
            "Selected 1: 'Protein'\n",
            "Select group for output\n",
            "Selected 1: 'Protein'\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "Note that major changes are planned in future for trjconv, to improve usability and utility.\n",
            "Select group for clustering\n",
            "Selected 1: 'Protein'\n",
            "Select group for output\n",
            "Selected 1: 'Protein'\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "Selected 4: 'Backbone'\n",
            "Selected 4: 'Backbone'\n",
            "Selected 3: 'C-alpha'\n"
          ]
        },
        {
          "output_type": "stream",
          "name": "stderr",
          "text": [
            "                     :-) GROMACS - gmx trjconv, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx trjconv, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx trjconv -s protein-ligand-out.tpr -f protein-ligand-out.xtc -o protein-ligand-out.pdb -pbc cluster\n",
            "\n",
            "Will write pdb: Protein data bank file\n",
            "Reading file protein-ligand-out.tpr, VERSION 2020.6 (single precision)\n",
            "Reading file protein-ligand-out.tpr, VERSION 2020.6 (single precision)\n",
            "Group     0 (         System) has 93935 elements\n",
            "Group     1 (        Protein) has  1695 elements\n",
            "Group     2 (      Protein-H) has  1301 elements\n",
            "Group     3 (        C-alpha) has   163 elements\n",
            "Group     4 (       Backbone) has   489 elements\n",
            "Group     5 (      MainChain) has   653 elements\n",
            "Group     6 (   MainChain+Cb) has   805 elements\n",
            "Group     7 (    MainChain+H) has   815 elements\n",
            "Group     8 (      SideChain) has   880 elements\n",
            "Group     9 (    SideChain-H) has   648 elements\n",
            "Group    10 (    Prot-Masses) has  1695 elements\n",
            "Group    11 (    non-Protein) has 92240 elements\n",
            "Group    12 (          Other) has    10 elements\n",
            "Group    13 (            JZ4) has    10 elements\n",
            "Group    14 (             NA) has    86 elements\n",
            "Group    15 (             CL) has    92 elements\n",
            "Group    16 (          Water) has 92052 elements\n",
            "Group    17 (            SOL) has 92052 elements\n",
            "Group    18 (      non-Water) has  1883 elements\n",
            "Group    19 (            Ion) has   178 elements\n",
            "Group    20 (            JZ4) has    10 elements\n",
            "Group    21 (             NA) has    86 elements\n",
            "Group    22 (             CL) has    92 elements\n",
            "Group    23 ( Water_and_ions) has 92230 elements\n",
            "Select a group: Group     0 (         System) has 93935 elements\n",
            "Group     1 (        Protein) has  1695 elements\n",
            "Group     2 (      Protein-H) has  1301 elements\n",
            "Group     3 (        C-alpha) has   163 elements\n",
            "Group     4 (       Backbone) has   489 elements\n",
            "Group     5 (      MainChain) has   653 elements\n",
            "Group     6 (   MainChain+Cb) has   805 elements\n",
            "Group     7 (    MainChain+H) has   815 elements\n",
            "Group     8 (      SideChain) has   880 elements\n",
            "Group     9 (    SideChain-H) has   648 elements\n",
            "Group    10 (    Prot-Masses) has  1695 elements\n",
            "Group    11 (    non-Protein) has 92240 elements\n",
            "Group    12 (          Other) has    10 elements\n",
            "Group    13 (            JZ4) has    10 elements\n",
            "Group    14 (             NA) has    86 elements\n",
            "Group    15 (             CL) has    92 elements\n",
            "Group    16 (          Water) has 92052 elements\n",
            "Group    17 (            SOL) has 92052 elements\n",
            "Group    18 (      non-Water) has  1883 elements\n",
            "Group    19 (            Ion) has   178 elements\n",
            "Group    20 (            JZ4) has    10 elements\n",
            "Group    21 (             NA) has    86 elements\n",
            "Group    22 (             CL) has    92 elements\n",
            "Group    23 ( Water_and_ions) has 92230 elements\n",
            "Select a group: \rReading frame       0 time    0.000   \n",
            "Precision of protein-ligand-out.xtc is 0.001 (nm)\n",
            " ->  frame      0 time    0.000      \r\rReading frame       1 time   10.000    ->  frame      1 time   10.000      \r\rReading frame       2 time   20.000    ->  frame      2 time   20.000      \r\rReading frame       3 time   30.000    ->  frame      3 time   30.000      \r\rReading frame       4 time   40.000    ->  frame      4 time   40.000      \r\rReading frame       5 time   50.000    ->  frame      5 time   50.000      \r\rReading frame       6 time   60.000    ->  frame      6 time   60.000      \r\rReading frame       7 time   70.000    ->  frame      7 time   70.000      \r\rReading frame       8 time   80.000    ->  frame      8 time   80.000      \r\rReading frame       9 time   90.000    ->  frame      9 time   90.000      \r\rReading frame      10 time  100.000    ->  frame     10 time  100.000      \r\rReading frame      11 time  110.000   \rReading frame      12 time  120.000   \rReading frame      13 time  130.000   \rReading frame      14 time  140.000   \rReading frame      15 time  150.000   \rReading frame      16 time  160.000   \rReading frame      17 time  170.000   \rReading frame      18 time  180.000   \rReading frame      19 time  190.000   \rReading frame      20 time  200.000    ->  frame     20 time  200.000      \r\rLast frame         20 time  200.000   \n",
            "\n",
            "\n",
            "GROMACS reminds you: \"Art For Arts Sake, Money For Gods Sake\" (10 CC)\n",
            "\n",
            "                     :-) GROMACS - gmx trjconv, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx trjconv, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx trjconv -s protein-ligand-out.tpr -f protein-ligand-out.xtc -o protein-0-10ns.xtc -pbc cluster\n",
            "\n",
            "Will write xtc: Compressed trajectory (portable xdr format): xtc\n",
            "Reading file protein-ligand-out.tpr, VERSION 2020.6 (single precision)\n",
            "Reading file protein-ligand-out.tpr, VERSION 2020.6 (single precision)\n",
            "Group     0 (         System) has 93935 elements\n",
            "Group     1 (        Protein) has  1695 elements\n",
            "Group     2 (      Protein-H) has  1301 elements\n",
            "Group     3 (        C-alpha) has   163 elements\n",
            "Group     4 (       Backbone) has   489 elements\n",
            "Group     5 (      MainChain) has   653 elements\n",
            "Group     6 (   MainChain+Cb) has   805 elements\n",
            "Group     7 (    MainChain+H) has   815 elements\n",
            "Group     8 (      SideChain) has   880 elements\n",
            "Group     9 (    SideChain-H) has   648 elements\n",
            "Group    10 (    Prot-Masses) has  1695 elements\n",
            "Group    11 (    non-Protein) has 92240 elements\n",
            "Group    12 (          Other) has    10 elements\n",
            "Group    13 (            JZ4) has    10 elements\n",
            "Group    14 (             NA) has    86 elements\n",
            "Group    15 (             CL) has    92 elements\n",
            "Group    16 (          Water) has 92052 elements\n",
            "Group    17 (            SOL) has 92052 elements\n",
            "Group    18 (      non-Water) has  1883 elements\n",
            "Group    19 (            Ion) has   178 elements\n",
            "Group    20 (            JZ4) has    10 elements\n",
            "Group    21 (             NA) has    86 elements\n",
            "Group    22 (             CL) has    92 elements\n",
            "Group    23 ( Water_and_ions) has 92230 elements\n",
            "Select a group: Group     0 (         System) has 93935 elements\n",
            "Group     1 (        Protein) has  1695 elements\n",
            "Group     2 (      Protein-H) has  1301 elements\n",
            "Group     3 (        C-alpha) has   163 elements\n",
            "Group     4 (       Backbone) has   489 elements\n",
            "Group     5 (      MainChain) has   653 elements\n",
            "Group     6 (   MainChain+Cb) has   805 elements\n",
            "Group     7 (    MainChain+H) has   815 elements\n",
            "Group     8 (      SideChain) has   880 elements\n",
            "Group     9 (    SideChain-H) has   648 elements\n",
            "Group    10 (    Prot-Masses) has  1695 elements\n",
            "Group    11 (    non-Protein) has 92240 elements\n",
            "Group    12 (          Other) has    10 elements\n",
            "Group    13 (            JZ4) has    10 elements\n",
            "Group    14 (             NA) has    86 elements\n",
            "Group    15 (             CL) has    92 elements\n",
            "Group    16 (          Water) has 92052 elements\n",
            "Group    17 (            SOL) has 92052 elements\n",
            "Group    18 (      non-Water) has  1883 elements\n",
            "Group    19 (            Ion) has   178 elements\n",
            "Group    20 (            JZ4) has    10 elements\n",
            "Group    21 (             NA) has    86 elements\n",
            "Group    22 (             CL) has    92 elements\n",
            "Group    23 ( Water_and_ions) has 92230 elements\n",
            "Select a group: \rReading frame       0 time    0.000   \n",
            "Precision of protein-ligand-out.xtc is 0.001 (nm)\n",
            "Using output precision of 0.001 (nm)\n",
            " ->  frame      0 time    0.000      \r\rReading frame       1 time   10.000    ->  frame      1 time   10.000      \r\rReading frame       2 time   20.000    ->  frame      2 time   20.000      \r\rReading frame       3 time   30.000    ->  frame      3 time   30.000      \r\rReading frame       4 time   40.000    ->  frame      4 time   40.000      \r\rReading frame       5 time   50.000    ->  frame      5 time   50.000      \r\rReading frame       6 time   60.000    ->  frame      6 time   60.000      \r\rReading frame       7 time   70.000    ->  frame      7 time   70.000      \r\rReading frame       8 time   80.000    ->  frame      8 time   80.000      \r\rReading frame       9 time   90.000    ->  frame      9 time   90.000      \r\rReading frame      10 time  100.000    ->  frame     10 time  100.000      \r\rReading frame      11 time  110.000   \rReading frame      12 time  120.000   \rReading frame      13 time  130.000   \rReading frame      14 time  140.000   \rReading frame      15 time  150.000   \rReading frame      16 time  160.000   \rReading frame      17 time  170.000   \rReading frame      18 time  180.000   \rReading frame      19 time  190.000   \rReading frame      20 time  200.000    ->  frame     20 time  200.000      \r\rLast frame         20 time  200.000   \n",
            "\n",
            "\n",
            "GROMACS reminds you: \"It's 2040 now. Our President is a plant.\" (Ghostbusters 2016)\n",
            "\n",
            "                       :-) GROMACS - gmx rms, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx rms, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx rms -s protein-ligand-out.tpr -f protein-ligand-out.pdb -o protein-0-1-RMSD.xvg\n",
            "\n",
            "Reading file protein-ligand-out.tpr, VERSION 2020.6 (single precision)\n",
            "Reading file protein-ligand-out.tpr, VERSION 2020.6 (single precision)\n",
            "Select group for least squares fit\n",
            "Group     0 (         System) has 93935 elements\n",
            "Group     1 (        Protein) has  1695 elements\n",
            "Group     2 (      Protein-H) has  1301 elements\n",
            "Group     3 (        C-alpha) has   163 elements\n",
            "Group     4 (       Backbone) has   489 elements\n",
            "Group     5 (      MainChain) has   653 elements\n",
            "Group     6 (   MainChain+Cb) has   805 elements\n",
            "Group     7 (    MainChain+H) has   815 elements\n",
            "Group     8 (      SideChain) has   880 elements\n",
            "Group     9 (    SideChain-H) has   648 elements\n",
            "Group    10 (    Prot-Masses) has  1695 elements\n",
            "Group    11 (    non-Protein) has 92240 elements\n",
            "Group    12 (          Other) has    10 elements\n",
            "Group    13 (            JZ4) has    10 elements\n",
            "Group    14 (             NA) has    86 elements\n",
            "Group    15 (             CL) has    92 elements\n",
            "Group    16 (          Water) has 92052 elements\n",
            "Group    17 (            SOL) has 92052 elements\n",
            "Group    18 (      non-Water) has  1883 elements\n",
            "Group    19 (            Ion) has   178 elements\n",
            "Group    20 (            JZ4) has    10 elements\n",
            "Group    21 (             NA) has    86 elements\n",
            "Group    22 (             CL) has    92 elements\n",
            "Group    23 ( Water_and_ions) has 92230 elements\n",
            "Select a group: Select group for RMSD calculation\n",
            "Group     0 (         System) has 93935 elements\n",
            "Group     1 (        Protein) has  1695 elements\n",
            "Group     2 (      Protein-H) has  1301 elements\n",
            "Group     3 (        C-alpha) has   163 elements\n",
            "Group     4 (       Backbone) has   489 elements\n",
            "Group     5 (      MainChain) has   653 elements\n",
            "Group     6 (   MainChain+Cb) has   805 elements\n",
            "Group     7 (    MainChain+H) has   815 elements\n",
            "Group     8 (      SideChain) has   880 elements\n",
            "Group     9 (    SideChain-H) has   648 elements\n",
            "Group    10 (    Prot-Masses) has  1695 elements\n",
            "Group    11 (    non-Protein) has 92240 elements\n",
            "Group    12 (          Other) has    10 elements\n",
            "Group    13 (            JZ4) has    10 elements\n",
            "Group    14 (             NA) has    86 elements\n",
            "Group    15 (             CL) has    92 elements\n",
            "Group    16 (          Water) has 92052 elements\n",
            "Group    17 (            SOL) has 92052 elements\n",
            "Group    18 (      non-Water) has  1883 elements\n",
            "Group    19 (            Ion) has   178 elements\n",
            "Group    20 (            JZ4) has    10 elements\n",
            "Group    21 (             NA) has    86 elements\n",
            "Group    22 (             CL) has    92 elements\n",
            "Group    23 ( Water_and_ions) has 92230 elements\n",
            "Select a group: Reading frames from pdb file\rReading frame       0 time    0.000   \n",
            "WARNING: topology has 93935 atoms, whereas trajectory has 1695\n",
            " 'Protein in water t=  10.00000 step= 5000', 1695 atoms\n",
            "\rReading frame       1 time   10.000   \rReading frame       2 time   20.000   \rReading frame       3 time   30.000   \rReading frame       4 time   40.000   \rReading frame       5 time   50.000   \rReading frame       6 time   60.000   \rReading frame       7 time   70.000   \rReading frame       8 time   80.000   \rReading frame       9 time   90.000   \rReading frame      10 time  100.000   \rReading frame      11 time  110.000   \rReading frame      12 time  120.000   \rReading frame      13 time  130.000   \rReading frame      14 time  140.000   \rReading frame      15 time  150.000   \rReading frame      16 time  160.000   \rReading frame      17 time  170.000   \rReading frame      18 time  180.000   \rReading frame      19 time  190.000   \rReading frame      20 time  200.000   \rLast frame         20 time  200.000   \n",
            "\n",
            "GROMACS reminds you: \"It's 2040 now. Our President is a plant.\" (Ghostbusters 2016)\n",
            "\n",
            "                       :-) GROMACS - gmx rmsf, 2020.6 (-:\n",
            "\n",
            "                            GROMACS is written by:\n",
            "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
            "    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    \n",
            " Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     \n",
            "  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  \n",
            "  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis\n",
            "    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \n",
            "  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   \n",
            "    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   \n",
            "    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  \n",
            "   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen \n",
            " Christian Wennberg    Maarten Wolf      Artem Zhmurov   \n",
            "                           and the project leaders:\n",
            "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
            "\n",
            "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
            "Copyright (c) 2001-2019, The GROMACS development team at\n",
            "Uppsala University, Stockholm University and\n",
            "the Royal Institute of Technology, Sweden.\n",
            "check out http://www.gromacs.org for more information.\n",
            "\n",
            "GROMACS is free software; you can redistribute it and/or modify it\n",
            "under the terms of the GNU Lesser General Public License\n",
            "as published by the Free Software Foundation; either version 2.1\n",
            "of the License, or (at your option) any later version.\n",
            "\n",
            "GROMACS:      gmx rmsf, version 2020.6\n",
            "Executable:   /content/gromacs/bin/gmx\n",
            "Data prefix:  /content/gromacs\n",
            "Working dir:  /content/3htb\n",
            "Command line:\n",
            "  gmx rmsf -s protein-ligand-out.tpr -f protein-ligand-out.pdb -o protein-0-10ns-RMSF.xvg -res\n",
            "\n",
            "Reading file protein-ligand-out.tpr, VERSION 2020.6 (single precision)\n",
            "Reading file protein-ligand-out.tpr, VERSION 2020.6 (single precision)\n",
            "Select group(s) for root mean square calculation\n",
            "Group     0 (         System) has 93935 elements\n",
            "Group     1 (        Protein) has  1695 elements\n",
            "Group     2 (      Protein-H) has  1301 elements\n",
            "Group     3 (        C-alpha) has   163 elements\n",
            "Group     4 (       Backbone) has   489 elements\n",
            "Group     5 (      MainChain) has   653 elements\n",
            "Group     6 (   MainChain+Cb) has   805 elements\n",
            "Group     7 (    MainChain+H) has   815 elements\n",
            "Group     8 (      SideChain) has   880 elements\n",
            "Group     9 (    SideChain-H) has   648 elements\n",
            "Group    10 (    Prot-Masses) has  1695 elements\n",
            "Group    11 (    non-Protein) has 92240 elements\n",
            "Group    12 (          Other) has    10 elements\n",
            "Group    13 (            JZ4) has    10 elements\n",
            "Group    14 (             NA) has    86 elements\n",
            "Group    15 (             CL) has    92 elements\n",
            "Group    16 (          Water) has 92052 elements\n",
            "Group    17 (            SOL) has 92052 elements\n",
            "Group    18 (      non-Water) has  1883 elements\n",
            "Group    19 (            Ion) has   178 elements\n",
            "Group    20 (            JZ4) has    10 elements\n",
            "Group    21 (             NA) has    86 elements\n",
            "Group    22 (             CL) has    92 elements\n",
            "Group    23 ( Water_and_ions) has 92230 elements\n",
            "Select a group: Reading frames from pdb file\rReading frame       0 time    0.000    'Protein in water t=  10.00000 step= 5000', 1695 atoms\n",
            "\rReading frame       1 time   10.000   \rReading frame       2 time   20.000   \rReading frame       3 time   30.000   \rReading frame       4 time   40.000   \rReading frame       5 time   50.000   \rReading frame       6 time   60.000   \rReading frame       7 time   70.000   \rReading frame       8 time   80.000   \rReading frame       9 time   90.000   \rReading frame      10 time  100.000   \rReading frame      11 time  110.000   \rReading frame      12 time  120.000   \rReading frame      13 time  130.000   \rReading frame      14 time  140.000   \rReading frame      15 time  150.000   \rReading frame      16 time  160.000   \rReading frame      17 time  170.000   \rReading frame      18 time  180.000   \rReading frame      19 time  190.000   \rReading frame      20 time  200.000   \rLast frame         20 time  200.000   \n",
            "\n",
            "GROMACS reminds you: \"It's 2040 now. Our President is a plant.\" (Ghostbusters 2016)\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#@title Run this to copy the entire project to your drive. This will paste all the results in \"result\" in your original drive folder.\n",
        "#Warning!!!!\n",
        "#Check if you have enough space!\n",
        "!mkdir $Google_Drive_Path/result\n",
        "!cp -r $mdpath/* $Google_Drive_Path/result"
      ],
      "metadata": {
        "id": "6Vwfkr4RwIKV"
      },
      "execution_count": null,
      "outputs": []
    }
  ]
}