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simple_model.txt
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simple_model.txt
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/* exmpales followed:
/S7_surfaces/signal.txt
/S7_surfaces/unbounded_diffusion/emitter1.txt
/S99_more/neuron/neuron.txt
units: nm ms
*/
define ca_src 1
define ca_int 0.0001 #0.1 ca2+ per usec
define cam_src 25
define dfc_ca 600000
define stimtime 5
#define rm_camca
#define graph_on
#-------------General parameters-------
ifdefine graph_on
graphics opengl_good
graphic_iter 1
frame_thickness 0
frame_color 1 1 1
#grid_thickness 1
else
graphics none
endif
dim 3
accuracy 10
molperbox 1
#boxsize 1
boundaries 0 -50 50
boundaries 1 -50 50
boundaries 2 -50 50
time_start 0
time_stop stimtime
time_step 0.00001 #0.01 usec
#-------------Molecules----------------
species ca
species cam
species cam-ca1
species cam-ca2
species cam-ca3
species cam-ca4
molecule_lists calst camlst
mol_list ca calst
mol_list cam* camlst
ifdefine graph_on
display_size all 0.1
color ca red
color cam black
color cam-* cyan
endif
difc ca dfc_ca # nm^2 us^(-1)
difc cam* 50000 #50 nm^2 us^(-1) -> 50000 nm^2 ms^(-1)
define NT_on 2618000 #nm^3 us^(-1)
define NT_off 160
define NR_on 54400000
define NR_off 44
define CT_on 285600
define CT_off 2.6
define CR_on 42500
define CR_off 0.0130
define cam1_on 57018000 #NT_on+CT_on
define cam1_off 162.6 #NT_off+CT_off
define cam2_on 57346100 #NT_on+NR_on+CT_on+CR_on
define cam2_off 206.6130 #NT_off+NR_off+CT_off+CR_off
define cam3_on 328100 #NR_on+CR_on
define cam3_off 44.0130 #NR_off+CR_off
define cam4_on 328100 #NR_on+CR_on
define cam4_off 44.0130 #NR_off+CR_off
#------------surfaces------------------
start_surface shell
action both ca t
action both cam* r
color both grey 0.5
polygon both edge
panel sph 0 0 0 10 20 20 #nanodomain radius 10nm
end_surface
start_compartment nano
surface shell
point 0 0 0
end_compartment
#-----------reactions------------------
reaction cam1 ca + cam -> cam-ca1 cam1_on
reaction cam1r cam-ca1 -> ca + cam cam1_off
reaction cam2 ca + cam-ca1 -> cam-ca2 cam2_on
reaction cam2r cam-ca2 -> ca + cam-ca1 cam2_off
reaction cam3 ca + cam-ca2 -> cam-ca3 cam3_on
reaction cam3r cam-ca3 -> ca + cam-ca2 cam3_off
reaction cam4 ca + cam-ca3 -> cam-ca4 cam4_on
reaction cam4r cam-ca4 -> ca + cam-ca3 cam4_off
binding_radius cam1 6.98
binding_radius cam2 7.02
binding_radius cam3 0.040168
binding_radius cam4 0.040168
#------------molecules in compartment--
compartment_mol cam_src cam nano
compartment_mol 0 cam-ca1 nano
compartment_mol 0 cam-ca2 nano
compartment_mol 0 cam-ca3 nano
compartment_mol 0 cam-ca4 nano
#------------commands------------------
cmd i 0 stimtime ca_int pointsource ca ca_src 0 0 0 #single ca channel 0.0936 /usec ~ 0.03 pA#
#cmd e pointsource ca ca_src 0 0 0
ifdefine graph_on
text_display ca
text_display cam
text_display cam-ca1
text_display cam-ca2
text_display cam-ca3
text_display cam-ca4
cmd b pause
endif
output_root results_nokill/
output_files simplemodel_nano.txt
output_files simplemodel.txt
output_files ca_track.txt
#output_files ca_molpos.txt
#output_files ca_molct_x.txt
#output_files ca_molct_y.txt
#output_files ca_molct_z.txt
cmd e molcountincmpt nano simplemodel_nano.txt
cmd e molcount simplemodel.txt
cmd e molpos ca ca_molpos.txt
cmd e trackmol 1 ca_track.txt
#cmd e molcountspace ca x -50 50 25 -10 10 -10 10 0 ca_molct_x.txt
#cmd e molcountspace ca y -50 50 25 -10 10 -10 10 0 ca_molct_y.txt
#cmd e molcountspace ca z -50 50 25 -10 10 -10 10 0 ca_molct_z.txt
#cmd e writeVTK ../vtk/simplemodl
ifdefine rm_camca
cmd e killmol cam-ca4
endif
end_file