Save and write trajectory only output one molecule

[sli259]

Hi, I am running the opt_example code on a multi-molecule system (liquid) and find the output save_traj output each molecular trajectory in different time steps, instead of combine all molecules in one step. Is there a way to adjust the code so the trajectory will show all molecules?

[wwang2]

The example we show is on a gas-phase molecule (so just one molecule).
For a more interesting example, you can try our alanine dipeptide example: https://colab.research.google.com/github/wwang2/Coarse-Graining-Auto-encoders/blob/master/cgae_alanine_dipeptide_colab_walkthrough.ipynb