# Excluded volume test
# units um s um^-2
graphics none

dim 2
species S S1 K KS P PS1 Ki Pi 
max_mol 4000


boundaries 0 0 0.316 r
boundaries 1 0 0.316 r

time_start 0
time_stop 32000
time_step 0.000005

accuracy 10

# between 0.01 and 1 for proteins on membranes
difc all 0.01



molecule_lists Klist Plist
mol_list K Klist
# mol_list S  S1 S2 S3 S4 S5 S6 S7 S8 S9 S10 Slist
mol_list P Plist
# mol_list KS KS1 KS2 KS3 KS4 KS5 KS6 KS7 KS8 KS9 PS1 PS2 PS3 PS4 PS5 PS6 PS7 PS8 PS9 PS10 Clist

mol 99 K u u
mol 1 P u u
mol 1 S u u

reaction Kf0 K + S -> KS 
 

reaction Pf1 P + S1 -> PS1 


reaction Kb0 KS -> K + S 1



reaction Pb1 PS1 -> P + S1 1


reaction Kp0 KS -> Ki + S1  0.1

reaction Pp1 PS1 -> Pi + S  0.1


reaction Kact Ki -> K 1
reaction Pact Pi -> P 1

product_placement Kb0 unbindrad 0.005

product_placement Pb1 unbindrad 0.005


binding_radius Kf0  0.005 
binding_radius Pf1 0.005


reaction_probability Kf0  0.05 # is the probability of reaction in time interval of dt
reaction_probability Pf1  0.05 # is the probability of reaction in time interval of dt



reaction evr1 K + K -> K + K
binding_radius evr1 0.005
product_placement evr1 bounce 0.0055
reaction evr2 K + KS -> K + KS
binding_radius evr2 0.005
product_placement evr2 bounce 0.0055

reaction evr4 K + P -> K + P
binding_radius evr4 0.005
product_placement evr4 bounce 0.0055
reaction evr5 K + PS1 -> K + PS1
binding_radius evr5 0.005
product_placement evr5 bounce 0.0055

reaction evr7 K + Ki -> K + Ki
binding_radius evr7 0.005
product_placement evr7 bounce 0.0055
reaction evr8 K + Pi -> K + Pi
binding_radius evr8 0.005
product_placement evr8 bounce 0.0055
reaction evr9 KS + KS -> KS + KS
binding_radius evr9 0.005
product_placement evr9 bounce 0.0055

reaction evr11 KS + P -> KS + P
binding_radius evr11 0.005
product_placement evr11 bounce 0.0055
reaction evr12 KS + PS1 -> KS + PS1
binding_radius evr12 0.005
product_placement evr12 bounce 0.0055


reaction evr14 KS + Ki -> KS + Ki
binding_radius evr14 0.005
product_placement evr14 bounce 0.0055
reaction evr15 KS + Pi -> KS + Pi
binding_radius evr15 0.005
product_placement evr15 bounce 0.0055





reaction evr22 P + P -> P + P
binding_radius evr22 0.005
product_placement evr22 bounce 0.0055
reaction evr23 P + PS1 -> P + PS1
binding_radius evr23 0.005
product_placement evr23 bounce 0.0055

reaction evr25 P + Ki -> P + Ki
binding_radius evr25 0.005
product_placement evr25 bounce 0.0055
reaction evr26 P + Pi -> P + Pi
binding_radius evr26 0.005
product_placement evr26 bounce 0.0055
reaction evr27 PS1 + PS1 -> PS1 + PS1
binding_radius evr27 0.005
product_placement evr27 bounce 0.0055

reaction evr29 PS1 + Ki -> PS1 + Ki
binding_radius evr29 0.005
product_placement evr29 bounce 0.0055
reaction evr30 PS1 + Pi -> PS1 + Pi
binding_radius evr30 0.005
product_placement evr30 bounce 0.0055

reaction evr34 Ki + Ki -> Ki + Ki
binding_radius evr34 0.005
product_placement evr34 bounce 0.0055
reaction evr35 Ki + Pi -> Ki + Pi
binding_radius evr35 0.005
product_placement evr35 bounce 0.0055
reaction evr36 Pi + Pi -> Pi + Pi
binding_radius evr36 0.005
product_placement evr36 bounce 0.0055


output_files S1_control1.txt
cmd b molcountheader  S1_control1.txt
 cmd i 500 4000 0.4 molcount  S1_control1.txt

cmd @ 4000 killmol all 
cmd @ 4000 volumesource K 97 0 1 0 1
cmd @ 4000 volumesource P 3 0 1 0 1
cmd @ 4000 volumesource S 1 0 1 0 1
cmd i 4500 8000 0.4 molcount  S1_control1.txt

cmd @ 8000 killmol all 
cmd @ 8000 volumesource K 94 0 1 0 1
cmd @ 8000 volumesource P 6 0 1 0 1
cmd @ 8000 volumesource S 1 0 1 0 1
cmd i 8500 12000 0.4 molcount  S1_control1.txt

cmd @ 12000 killmol all 
cmd @ 12000 volumesource K 88 0 1 0 1
cmd @ 12000 volumesource P 12 0 1 0 1
cmd @ 12000 volumesource S 1 0 1 0 1
cmd i 12500 16000 0.4 molcount  S1_control1.txt

cmd @ 16000 killmol all 
cmd @ 16000 volumesource K 80 0 1 0 1
cmd @ 16000 volumesource P 20 0 1 0 1
cmd @ 16000 volumesource S 1 0 1 0 1
cmd i 16500 20000 0.4 molcount  S1_control1.txt

cmd @ 20000 killmol all 
cmd @ 20000 volumesource K 70 0 1 0 1
cmd @ 20000 volumesource P 30 0 1 0 1
cmd @ 20000 volumesource S 10 0 1 0 1
cmd i 20500 24000 0.4 molcount  S1_control1.txt

cmd @ 24000 killmol all 
cmd @ 24000 volumesource K 60 0 1 0 1
cmd @ 24000 volumesource P 40 0 1 0 1
cmd @ 24000 volumesource S 10 0 1 0 1
cmd i 24500 28000 0.4 molcount  S1_control1.txt

cmd @ 28000 killmol all 
cmd @ 28000 volumesource K 50 0 1 0 1
cmd @ 28000 volumesource P 50 0 1 0 1
cmd @ 28000 volumesource S 10 0 1 0 1
cmd i 28500 32000 0.4 molcount  S1_control1.txt



end_file