Commit bdd36948 authored by Urban BEZELJAK's avatar Urban BEZELJAK

Uploaded configuration files

parent 0406c9b8
# File Rab5config.csv, by Urban Bezeljak.
# Rab5 activation network
# units are micrometer, second
#### To run, "| cd C:\Program Files\Smoldyn |" then "| smoldyn "C:\PhD\Model\200325_Rab5config.csv" |".
define SIMnum 1
define GEFnum 20
#Parameters
#Diffusion coefficients
define D_sol 10 # Protein diffusion coefficient in solution (um^2/s) Halatek2018
define D_mem 0.3 # Protein diffusion coefficient on membrane (um^2/s)
#Reaction rates
define k_1 0.01 # RabGDP:GDI complex dissociation rate (s^-1)
define k_2 0.00007 # RabGDP:GDI complex association rate (um^3/s)
define k_3 0.00050 # Rab5 intrinsic GTPase activity (s^-1)
define k_4 0.000003 # Basal RR activatopn rate (um^3/s)
define k_5 0.00003 # Rab5GTP:RR complex association rate (um^3/s)
define k_6 0.1 # Rab5GTP:RR complex dissociation rate (s^-1)
define k_7 0.01 # Positive feedback Rab5 activation rate (um^3/s)
define k_8 0.00015 # GDI extraction rate (um^3/s)
define k_rab 10 # Rab5 adsorption to the membrane (um/s)
define k_rr_on 0.01 # RR adsorption to the membrane (um/s)
define k_rr_off 1 # Rabex5 desorptoin from the membrane (s^-1)
#Inital numbers
define N_Rab5GTP 0 # number of Rab5GTP on the membrane
define N_Rab5GDP 0
define N_Rab5GDP:GDI 1000 # number of Rab5GDP:GDI in solution
define N_GDI 4000 # number of free GDI in solution
define N_RR GEFnum # number of Rabex5:Rabaptin5 in solution
define N_Rab5RR 0
# define N_GAP 200 # number of GAP in solution
#Simulation
define t_STOP 12600 # stopping time
# graphics none
graphics opengl
#graphic_iter 1000
#tiff_iter 10000
#Geometry
dim 3
boundaries x 0 4 p
boundaries y 0 4 p
boundaries z 0 0.2 p
frame_thickness 0
time_start 0
time_stop t_STOP
time_step 0.05 # 50 ms time step (default from User manual)
accuracy 5
molperbox 4
#List of molecular species
species Rab5GDP
species Rab5GTP
species Rab5GDP:GDI
species GDI
species RR
species Rab5GTP:RR
molecule_lists list1 list2 list3 list4 list5 list6 #molecule list to speed up the simulation
mol_list Rab5GDP(all) list1
mol_list Rab5GTP(all) list2
mol_list Rab5GDP:GDI(fsoln) list3
mol_list GDI(all) list4
mol_list RR(all) list5
mol_list Rab5GTP:RR(all) list6
difc Rab5GDP(front) D_mem
difc Rab5GDP(fsoln) D_sol
difc Rab5GTP(front) D_mem
difc GDI(fsoln) D_sol
difc Rab5GDP:GDI(fsoln) D_sol
difc RR(fsoln) D_sol
difc RR(front) D_mem
difc Rab5GTP:RR(front) D_mem
color Rab5GDP(front) red
color Rab5GTP(front) green
color GDI(fsoln) orange
color Rab5GDP:GDI(fsoln) rose
color RR(fsoln) lightblue
color RR(front) blue
color Rab5GTP:RR(front) purple
display_size all(solution) 3
display_size all(front) 7
start_surface walls
color both 0 0 1 0.05
action both all reflect
panel rect +x 0 0 0 4 0.2
panel rect -x 4 0 0 4 0.2
panel rect -y 0 0 0 4 0.2
panel rect +y 0 4 0 4 0.2
panel rect +z 0 0 0.2 4 4
end_surface
start_surface membrane
action both all reflect
neighbor_action stay
rate Rab5GDP fsoln front k_rab
rate RR fsoln front k_rr_on
rate RR front fsoln k_rr_off
color both 0 0 1 1.0
polygon both edge
panel rect +z 0 0 0 0.8 0.8
panel rect +z 0 0.8 0 0.8 0.8
panel rect +z 0.8 0 0 0.8 0.8
panel rect +z 0.8 0.8 0 0.8 0.8
panel rect +z 0.8 1.6 0 0.8 0.8
panel rect +z 1.6 0.8 0 0.8 0.8
panel rect +z 0 1.6 0 0.8 0.8
panel rect +z 1.6 0 0 0.8 0.8
panel rect +z 1.6 1.6 0 0.8 0.8
panel rect +z 1.6 2.4 0 0.8 0.8
panel rect +z 2.4 1.6 0 0.8 0.8
panel rect +z 0.8 2.4 0 0.8 0.8
panel rect +z 2.4 0.8 0 0.8 0.8
panel rect +z 0 2.4 0 0.8 0.8
panel rect +z 2.4 0 0 0.8 0.8
panel rect +z 2.4 2.4 0 0.8 0.8
panel rect +z 0.8 3.2 0 0.8 0.8
panel rect +z 3.2 0.8 0 0.8 0.8
panel rect +z 1.6 3.2 0 0.8 0.8
panel rect +z 3.2 1.6 0 0.8 0.8
panel rect +z 2.4 3.2 0 0.8 0.8
panel rect +z 3.2 2.4 0 0.8 0.8
panel rect +z 3.2 3.2 0 0.8 0.8
panel rect +z 3.2 0 0 0.8 0.8
panel rect +z 0 3.2 0 0.8 0.8
end_surface
#Reactions
reaction rxn_1_1 Rab5GDP:GDI(fsoln) <-> Rab5GDP(fsoln) + GDI(fsoln) k_1 k_2
product_placement rxn_1_1fwd pgemmax 0.9
reaction rxn_1_2 Rab5GDP(front) + GDI(fsoln) -> Rab5GDP:GDI(fsoln) k_8
reaction rxn_2 Rab5GTP(front) -> Rab5GDP(front) k_3
reaction rxn_3_1 Rab5GDP(front) + RR(fsoln) -> Rab5GTP(front) + RR(fsoln) k_4
reaction rxn_3_2 Rab5GDP(front) + RR(front) -> Rab5GTP(front) + RR(fsoln) k_4
reaction rxn_4_1 Rab5GTP(front) + RR(fsoln) <-> Rab5GTP:RR(front) k_5 k_6
reaction rxn_4_2 Rab5GTP(front) + RR(front) <-> Rab5GTP:RR(front) k_5 k_6
reaction rxn_5_2 Rab5GTP:RR(front) + Rab5GDP(front) -> Rab5GTP:RR(front) + Rab5GTP(front) k_7
reaction_serialnum rxn_5_2 r1 + new
reaction_log output_rxn5_200325sim_GEFnum_SIMnum.csv rxn_5_2 all
### CROWDING
reaction crowding3 Rab5GTP(front) + Rab5GTP(front) -> Rab5GTP(front) + Rab5GTP(front)
binding_radius crowding3 0.005
product_placement crowding3 bounce
mol N_Rab5GDP:GDI Rab5GDP:GDI(fsoln) u u u
mol N_GDI GDI(fsoln) u u u
mol N_RR RR(fsoln) u u u
surface_mol N_Rab5GTP Rab5GTP(front) membrane all all
surface_mol N_Rab5GDP Rab5GDP(front) membrane all all
surface_mol N_Rab5RR Rab5GTP:RR(front) membrane all all
# Equilibarate the system in the 1st minute
cmd i 0 59 1 fixmolcount RR 0
cmd @ 60 fixmolcount RR N_RR
# Maintain the molecule count during first 500 activated Rab molecules
cmd e ifless Rab5GTP(front) 500 fixmolcount Rab5GDP:GDI N_Rab5GDP:GDI
cmd e ifless Rab5GTP(front) 500 fixmolcountrange GDI N_GDI N_GDI+N_Rab5GDP:GDI
text_display time Rab5GDP(front) Rab5GTP(all) Rab5GDP:GDI(all) GDI(all) RR(all) Rab5GTP:RR(all)
# output_root results\200325\
# output_files output_molcount_200325sim_SIMnum_GEFnum.csv output_molpos_RabGTP_200325sim_GEFnum_SIMnum.csv output_molpos_RabGTPRR_200325sim_GEFnum_SIMnum.csv output_molpos_RR_200325sim_GEFnum_SIMnum.csv output_molpos_RabGDP_200325sim_GEFnum_SIMnum.csv
# output_files output_restime_RabGTP_200325sim_GEFnum_SIMnum.csv output_restime_RabGDP_200325sim_GEFnum_SIMnum.csv output_rxn5_200325sim_GEFnum_SIMnum.csv
# cmd b molcountheader output_molcount_200325sim_SIMnum_GEFnum.csv
# output_format csv
# cmd n 100 molcount output_molcount_200325sim_SIMnum_GEFnum.csv
# cmd n 500 molpos Rab5GTP(front) output_molpos_RabGTP_200325sim_GEFnum_SIMnum.csv
# cmd n 500 molpos Rab5GTP:RR(front) output_molpos_RabGTPRR_200325sim_GEFnum_SIMnum.csv
# cmd n 500 molpos RR(front) output_molpos_RR_200325sim_GEFnum_SIMnum.csv
# cmd n 500 molpos Rab5GDP(front) output_molpos_RabGDP_200325sim_GEFnum_SIMnum.csv
# cmd e residencetime Rab5GTP(front) a e 0 5 500 output_restime_RabGTP_200325sim_GEFnum_SIMnum.csv
# cmd e residencetime Rab5GDP(front) a e 0 5 500 output_restime_RabGDP_200325sim_GEFnum_SIMnum.csv
cmd n 2000 executiontime stdout
end_file
# File Rab5config.csv, by Urban Bezeljak.
# Rab5 activation network
# units are micrometer, second
#### To run, "| cd C:\Program Files\Smoldyn |" then "| smoldyn "C:\PhD\Model\2004011_Rab5config.csv" |".
define SIMnum 1
define GEFnum 20
#Parameters
#Diffusion coefficients
define D_sol 10 # Protein diffusion coefficient in solution (um^2/s) Halatek2018
define D_mem 0.3 # Protein diffusion coefficient on membrane (um^2/s)
#Reaction rates
define k_1 0.01 # RabGDP:GDI complex dissociation rate (s^-1)
define k_2 0.00007 # RabGDP:GDI complex association rate (um^3/s)
define k_3 0.00050 # Rab5 intrinsic GTPase activity (s^-1)
define k_4 0.000003 # Basal RR activatopn rate (um^3/s)
define k_5 0.00003 # Rab5GTP:RR complex association rate (um^3/s)
define k_6 0.1 # Rab5GTP:RR complex dissociation rate (s^-1)
define k_7 0.01 # Positive feedback Rab5 activation rate (um^3/s)
define k_8 0.00015 # GDI extraction rate (um^3/s)
define k_rab 10 # Rab5 adsorption to the membrane (um/s)
define k_rr_on 0.01 # RR adsorption to the membrane (um/s)
define k_rr_off 1 # Rabex5 desorptoin from the membrane (s^-1)
#Inital numbers
define N_Rab5GTP 0 # number of Rab5GTP on the membrane
define N_Rab5GDP 0
define N_Rab5GDP:GDI 1000 # number of Rab5GDP:GDI in solution
define N_GDI 4000 # number of free GDI in solution
define N_RR GEFnum # number of Rabex5:Rabaptin5 in solution
define N_Rab5RR 0
#Simulation
define t_STOP 12600 # stopping time
# graphics none
graphics opengl
#graphic_iter 1000
#tiff_iter 10000
#Geometry
dim 3
boundaries x 0 4 p
boundaries y 0 4 p
boundaries z 0 0.2 p
frame_thickness 0
time_start 0
time_stop t_STOP
time_step 0.05 # 50 ms time step (default from User manual)
accuracy 5
molperbox 4
#List of molecular species
species Rab5GDP
species Rab5GTP
species Rab5GDP:GDI
species GDI
species RR
species Rab5GTP:RR
molecule_lists list1 list2 list3 list4 list5 list6 #molecule list to speed up the simulation
mol_list Rab5GDP(all) list1
mol_list Rab5GTP(all) list2
mol_list Rab5GDP:GDI(fsoln) list3
mol_list GDI(all) list4
mol_list RR(all) list5
mol_list Rab5GTP:RR(all) list6
difc Rab5GDP(front) D_mem
difc Rab5GDP(fsoln) D_sol
difc Rab5GTP(front) D_mem
difc GDI(fsoln) D_sol
difc Rab5GDP:GDI(fsoln) D_sol
difc RR(fsoln) D_sol
difc RR(front) D_mem
difc Rab5GTP:RR(front) D_mem
color Rab5GDP(front) red
color Rab5GTP(front) green
color GDI(fsoln) orange
color Rab5GDP:GDI(fsoln) rose
color RR(fsoln) lightblue
color RR(front) blue
color Rab5GTP:RR(front) purple
display_size all(solution) 3
display_size all(front) 7
start_surface walls
color both 0 0 1 0.05
action both all reflect
panel rect +x 0 0 0 4 0.2
panel rect -x 4 0 0 4 0.2
panel rect -y 0 0 0 4 0.2
panel rect +y 0 4 0 4 0.2
panel rect +z 0 0 0.2 4 4
end_surface
start_surface membrane
action both all reflect
neighbor_action stay
rate Rab5GDP fsoln front k_rab
rate RR fsoln front k_rr_on
rate RR front fsoln k_rr_off
color both 0 0 1 1.0
polygon both edge
panel rect +z 0 0 0 4 4
# panel rect +z 0 2 0 2 2
# panel rect +z 2 0 0 2 2
# panel rect +z 2 2 0 2 2
# panel rect +z 2 4 0 2 2
# panel rect +z 4 2 0 2 2
# panel rect +z 0 4 0 2 2
# panel rect +z 4 0 0 2 2
# panel rect +z 4 4 0 2 2
end_surface
#Reactions
reaction rxn_1_1 Rab5GDP:GDI(fsoln) <-> Rab5GDP(fsoln) + GDI(fsoln) k_1 k_2
product_placement rxn_1_1fwd pgemmax 0.9
reaction rxn_1_2 Rab5GDP(front) + GDI(fsoln) -> Rab5GDP:GDI(fsoln) k_8
reaction rxn_2 Rab5GTP(front) -> Rab5GDP(front) k_3
reaction rxn_3_1 Rab5GDP(front) + RR(fsoln) -> Rab5GTP(front) + RR(fsoln) k_4
reaction rxn_3_2 Rab5GDP(front) + RR(front) -> Rab5GTP(front) + RR(fsoln) k_4
reaction rxn_4_1 Rab5GTP(front) + RR(fsoln) <-> Rab5GTP:RR(front) k_5 k_6
reaction rxn_4_2 Rab5GTP(front) + RR(front) <-> Rab5GTP:RR(front) k_5 k_6
reaction rxn_5_2 Rab5GTP:RR(front) + Rab5GDP(front) -> Rab5GTP:RR(front) + Rab5GTP(front) k_7
reaction_serialnum rxn_5_2 r1 + new
reaction_log output_rxn5_2004011sim_GEFnum_SIMnum.csv rxn_5_2 all
### CROWDING
reaction crowding3 Rab5GTP(front) + Rab5GTP(front) -> Rab5GTP(front) + Rab5GTP(front)
binding_radius crowding3 0.005
product_placement crowding3 bounce
mol N_Rab5GDP:GDI Rab5GDP:GDI(fsoln) u u u
mol N_GDI GDI(fsoln) u u u
mol N_RR RR(fsoln) u u u
surface_mol N_Rab5GTP Rab5GTP(front) membrane all all
surface_mol N_Rab5GDP Rab5GDP(front) membrane all all
surface_mol N_Rab5RR Rab5GTP:RR(front) membrane all all
# Equilibarate the system in the 1st minute
cmd i 0 59 1 fixmolcount RR 0
cmd @ 60 fixmolcount RR N_RR
# Maintain the molecule count during first 500 active Rab5
cmd e ifless Rab5GTP(front) 500 fixmolcount Rab5GDP:GDI N_Rab5GDP:GDI
cmd e ifless Rab5GTP(front) 500 fixmolcountrange GDI N_GDI N_GDI+N_Rab5GDP:GDI
text_display time Rab5GDP(front) Rab5GTP(all) Rab5GDP:GDI(all) GDI(all) RR(all) Rab5GTP:RR(all)
output_root results\2004011\
output_files output_molcount_2004011sim_SIMnum_GEFnum.csv output_molpos_RabGTP_2004011sim_GEFnum_SIMnum.csv output_molpos_RabGTPRR_2004011sim_GEFnum_SIMnum.csv output_molpos_RR_2004011sim_GEFnum_SIMnum.csv output_molpos_RabGDP_2004011sim_GEFnum_SIMnum.csv
output_files output_restime_RabGTP_2004011sim_GEFnum_SIMnum.csv output_restime_RabGDP_2004011sim_GEFnum_SIMnum.csv output_rxn5_2004011sim_GEFnum_SIMnum.csv
cmd b molcountheader output_molcount_2004011sim_SIMnum_GEFnum.csv
output_format csv
cmd n 100 molcount output_molcount_2004011sim_SIMnum_GEFnum.csv
cmd n 500 molpos Rab5GTP(front) output_molpos_RabGTP_2004011sim_GEFnum_SIMnum.csv
cmd n 500 molpos Rab5GTP:RR(front) output_molpos_RabGTPRR_2004011sim_GEFnum_SIMnum.csv
cmd n 500 molpos RR(front) output_molpos_RR_2004011sim_GEFnum_SIMnum.csv
cmd n 500 molpos Rab5GDP(front) output_molpos_RabGDP_2004011sim_GEFnum_SIMnum.csv
cmd e residencetime Rab5GTP(front) a e 0 5 500 output_restime_RabGTP_2004011sim_GEFnum_SIMnum.csv
cmd e residencetime Rab5GDP(front) a e 0 5 500 output_restime_RabGDP_2004011sim_GEFnum_SIMnum.csv
cmd n 2000 executiontime stdout
end_file
# File Rab5config.csv, by Urban Bezeljak.
# Rab5 activation network
# units are micrometer, second
#### To run, "| cd C:\Program Files\Smoldyn |" then "| smoldyn "C:\PhD\Model\2004012_Rab5config.csv" |".
define SIMnum 1
define GEFnum 20
#Parameters
#Diffusion coefficients
define D_sol 10 # Protein diffusion coefficient in solution (um^2/s) Halatek2018
define D_mem 0.3 # Protein diffusion coefficient on membrane (um^2/s)
#Reaction rates
define k_1 0.01 # RabGDP:GDI complex dissociation rate (s^-1)
define k_2 0.00007 # RabGDP:GDI complex association rate (um^3/s)
define k_3 0.00050 # Rab5 intrinsic GTPase activity (s^-1)
define k_4 0.000003 # Basal RR activatopn rate (um^3/s)
define k_5 0.00003 # Rab5GTP:RR complex association rate (um^3/s)
define k_6 0.1 # Rab5GTP:RR complex dissociation rate (s^-1)
define k_7 0.01 # Positive feedback Rab5 activation rate (um^3/s)
define k_8 0.00015 # GDI extraction rate (um^3/s)
define k_rab 10 # Rab5 adsorption to the membrane (um/s)
define k_rr_on 0.01 # RR adsorption to the membrane (um/s)
define k_rr_off 1 # Rabex5 desorptoin from the membrane (s^-1)
#Inital numbers
define N_Rab5GTP 0 # number of Rab5GTP on the membrane
define N_Rab5GDP 0
define N_Rab5GDP:GDI 1000 # number of Rab5GDP:GDI in solution
define N_GDI 4000 # number of free GDI in solution
define N_RR GEFnum # number of Rabex5:Rabaptin5 in solution
define N_Rab5RR 0
#Simulation
define t_STOP 12600 # stopping time
# graphics none
graphics opengl
#graphic_iter 1000
#tiff_iter 10000
#Geometry
dim 3
boundaries x 0 4 p
boundaries y 0 4 p
boundaries z 0 0.2 p
frame_thickness 0
time_start 0
time_stop t_STOP
time_step 0.05 # 10 ms time step (default from User manual)
accuracy 5
molperbox 4
#List of molecular species
species Rab5GDP
species Rab5GTP
species Rab5GDP:GDI
species GDI
species RR
species Rab5GTP:RR
molecule_lists list1 list2 list3 list4 list5 list6 #molecule list to speed up the simulation
mol_list Rab5GDP(all) list1
mol_list Rab5GTP(all) list2
mol_list Rab5GDP:GDI(fsoln) list3
mol_list GDI(all) list4
mol_list RR(all) list5
mol_list Rab5GTP:RR(all) list6
difc Rab5GDP(front) D_mem
difc Rab5GDP(fsoln) D_sol
difc Rab5GTP(front) D_mem
difc GDI(fsoln) D_sol
difc Rab5GDP:GDI(fsoln) D_sol
difc RR(fsoln) D_sol
difc RR(front) D_mem
difc Rab5GTP:RR(front) D_mem
color Rab5GDP(front) red
color Rab5GTP(front) green
color GDI(fsoln) orange
color Rab5GDP:GDI(fsoln) rose
color RR(fsoln) lightblue
color RR(front) blue
color Rab5GTP:RR(front) purple
display_size all(solution) 3
display_size all(front) 7
start_surface walls
color both 0 0 1 0.05
action both all reflect
panel rect +x 0 0 0 4 0.2
panel rect -x 4 0 0 4 0.2
panel rect -y 0 0 0 4 0.2
panel rect +y 0 4 0 4 0.2
panel rect +z 0 0 0.2 4 4
end_surface
start_surface membrane
action both all reflect
neighbor_action stay
rate Rab5GDP fsoln front k_rab
rate RR fsoln front k_rr_on
rate RR front fsoln k_rr_off
color both 0 0 1 1.0
polygon both edge
panel rect +z 0 0 0 2 2
panel rect +z 0 2 0 2 2
panel rect +z 2 0 0 2 2
panel rect +z 2 2 0 2 2
# panel rect +z 2 4 0 2 2
# panel rect +z 4 2 0 2 2
# panel rect +z 0 4 0 2 2
# panel rect +z 4 0 0 2 2
# panel rect +z 4 4 0 2 2
end_surface
#Reactions
reaction rxn_1_1 Rab5GDP:GDI(fsoln) <-> Rab5GDP(fsoln) + GDI(fsoln) k_1 k_2
product_placement rxn_1_1fwd pgemmax 0.9
reaction rxn_1_2 Rab5GDP(front) + GDI(fsoln) -> Rab5GDP:GDI(fsoln) k_8
reaction rxn_2 Rab5GTP(front) -> Rab5GDP(front) k_3
reaction rxn_3_1 Rab5GDP(front) + RR(fsoln) -> Rab5GTP(front) + RR(fsoln) k_4
reaction rxn_3_2 Rab5GDP(front) + RR(front) -> Rab5GTP(front) + RR(fsoln) k_4
reaction rxn_4_1 Rab5GTP(front) + RR(fsoln) <-> Rab5GTP:RR(front) k_5 k_6
reaction rxn_4_2 Rab5GTP(front) + RR(front) <-> Rab5GTP:RR(front) k_5 k_6
reaction rxn_5_2 Rab5GTP:RR(front) + Rab5GDP(front) -> Rab5GTP:RR(front) + Rab5GTP(front) k_7
reaction_serialnum rxn_5_2 r1 + new
reaction_log output_rxn5_2004012sim_GEFnum_SIMnum.csv rxn_5_2 all
### CROWDING
reaction crowding3 Rab5GTP(front) + Rab5GTP(front) -> Rab5GTP(front) + Rab5GTP(front)
binding_radius crowding3 0.005
product_placement crowding3 bounce
mol N_Rab5GDP:GDI Rab5GDP:GDI(fsoln) u u u
mol N_GDI GDI(fsoln) u u u
mol N_RR RR(fsoln) u u u
surface_mol N_Rab5GTP Rab5GTP(front) membrane all all
surface_mol N_Rab5GDP Rab5GDP(front) membrane all all
surface_mol N_Rab5RR Rab5GTP:RR(front) membrane all all
# Equilibarate the system in the 1st minute
cmd i 0 59 1 fixmolcount RR 0
cmd @ 60 fixmolcount RR N_RR
# Maintain the molecule count during first 500 active Rab5
cmd e ifless Rab5GTP(front) 500 fixmolcount Rab5GDP:GDI N_Rab5GDP:GDI
cmd e ifless Rab5GTP(front) 500 fixmolcountrange GDI N_GDI N_GDI+N_Rab5GDP:GDI
text_display time Rab5GDP(front) Rab5GTP(all) Rab5GDP:GDI(all) GDI(all) RR(all) Rab5GTP:RR(all)
output_root results\2004012\
output_files output_molcount_2004012sim_SIMnum_GEFnum.csv output_molpos_RabGTP_2004012sim_GEFnum_SIMnum.csv output_molpos_RabGTPRR_2004012sim_GEFnum_SIMnum.csv output_molpos_RR_2004012sim_GEFnum_SIMnum.csv output_molpos_RabGDP_2004012sim_GEFnum_SIMnum.csv
output_files output_restime_RabGTP_2004012sim_GEFnum_SIMnum.csv output_restime_RabGDP_2004012sim_GEFnum_SIMnum.csv output_rxn5_2004012sim_GEFnum_SIMnum.csv
cmd b molcountheader output_molcount_2004012sim_SIMnum_GEFnum.csv
output_format csv
cmd n 100 molcount output_molcount_2004012sim_SIMnum_GEFnum.csv
cmd n 500 molpos Rab5GTP(front) output_molpos_RabGTP_2004012sim_GEFnum_SIMnum.csv
cmd n 500 molpos Rab5GTP:RR(front) output_molpos_RabGTPRR_2004012sim_GEFnum_SIMnum.csv
cmd n 500 molpos RR(front) output_molpos_RR_2004012sim_GEFnum_SIMnum.csv
cmd n 500 molpos Rab5GDP(front) output_molpos_RabGDP_2004012sim_GEFnum_SIMnum.csv
cmd e residencetime Rab5GTP(front) a e 0 5 500 output_restime_RabGTP_2004012sim_GEFnum_SIMnum.csv
cmd e residencetime Rab5GDP(front) a e 0 5 500 output_restime_RabGDP_2004012sim_GEFnum_SIMnum.csv
cmd n 2000 executiontime stdout
end_file
# File Rab5config.csv, by Urban Bezeljak.
# Rab5 activation network
# units are micrometer, second
#### To run, "| cd C:\Program Files\Smoldyn |" then "| smoldyn "C:\PhD\Model\2004013_Rab5config.csv" |".
define SIMnum 1
define GEFnum 20
#Parameters
#Diffusion coefficients
define D_sol 10 # Protein diffusion coefficient in solution (um^2/s) Halatek2018
define D_mem 0.3 # Protein diffusion coefficient on membrane (um^2/s)
#Reaction rates
define k_1 0.01 # RabGDP:GDI complex dissociation rate (s^-1)
define k_2 0.00007 # RabGDP:GDI complex association rate (um^3/s)
define k_3 0.00050 # Rab5 intrinsic GTPase activity (s^-1)
define k_4 0.000003 # Basal RR activatopn rate (um^3/s)
define k_5 0.00003 # Rab5GTP:RR complex association rate (um^3/s)
define k_6 0.1 # Rab5GTP:RR complex dissociation rate (s^-1)
define k_7 0.01 # Positive feedback Rab5 activation rate (um^3/s)
define k_8 0.00015 # GDI extraction rate (um^3/s)
define k_rab 10 # Rab5 adsorption to the membrane (um/s)
define k_rr_on 0.01 # RR adsorption to the membrane (um/s)
define k_rr_off 1 # Rabex5 desorptoin from the membrane (s^-1)
#Inital numbers
define N_Rab5GTP 0 # number of Rab5GTP on the membrane
define N_Rab5GDP 0
define N_Rab5GDP:GDI 1000 # number of Rab5GDP:GDI in solution
define N_GDI 4000 # number of free GDI in solution
define N_RR GEFnum # number of Rabex5:Rabaptin5 in solution
define N_Rab5RR 0
#Simulation
define t_STOP 12600 # stopping time
# graphics none
graphics opengl
#graphic_iter 1000
#tiff_iter 10000
#Geometry
dim 3
boundaries x 0 4 p
boundaries y 0 4 p
boundaries z 0 0.2 p
frame_thickness 0
time_start 0
time_stop t_STOP
time_step 0.05 # 50 ms time step (default from User manual)
accuracy 5
molperbox 4
#List of molecular species
species Rab5GDP
species Rab5GTP
species Rab5GDP:GDI
species GDI
species RR
species Rab5GTP:RR
molecule_lists list1 list2 list3 list4 list5 list6 #molecule list to speed up the simulation
mol_list Rab5GDP(all) list1
mol_list Rab5GTP(all) list2
mol_list Rab5GDP:GDI(fsoln) list3
mol_list GDI(all) list4
mol_list RR(all) list5
mol_list Rab5GTP:RR(all) list6
difc Rab5GDP(front) D_mem
difc Rab5GDP(fsoln) D_sol
difc Rab5GTP(front) D_mem