# E-coli BamA simulation file

graphics opengl_good
dim 3
species BamA RcsF IgaA OmpA [OmpA] BamA-RcsF OmpA-RcsF IgaA-RcsF BamA-RcsF-[OmpA]


time_start 0
time_stop 500
time_step 0.1

color BamA maroon
color RcsF red
color IgaA olive
color OmpA sky
color [OmpA] violet
color BamA-rcsF rose
color OmpA-RcsF yellow
color IgaA-RcsF aqua
color BamA-RcsF-[OmpA] grey

display_size BamA 1
display_size RcsF 1
display_size IgaA 1
display_size OmpA 1
display_size [OmpA] 1
display_size BamA-RcsF 1
display_size OmpA-RcsF 1
display_size IgaA-RcsF 1
display_size BamA-RcsF-[OmpA]1

boundaries 0 0 500 r
boundaries 1 0 100 r
boundaries 2 0 100 r

mol 3900 BamA u u u
mol 3100 RcsF u u 9
mol 200 IgaA 0 u u
mol 210000 [OmpA] u u u

difc BamA 100
difc RcsF 10
difc [OmpA] 10

reaction BamA + RcsF -> BamA-RcsF 3e-2
reaction BamA-RcsF + OmpA -> BamA + OmpA-RcsF 5e2
reaction BamA + [OmpA] -> OmpA 4e-8
reaction BamA + RcsF + [OmpA] -> BamA-RcsF-[OmpA] 4e-2
reaction BamA-RcsF-[OmpA] -> BamA + OmpA-RcsF 6e-2
reaction RcsF + IgaA -> IgaA-RcsF 8e-2
reaction X -> BamA 1e0
reaction X -> RcsF 1e0
reaction X -> IgaA 10e-1
reaction X -> [OmpA] 1e3


end_file

