# Smoldyn configuration file to run abba.bngl BioNetGen network.

random_seed 1

# Graphical output
graphics opengl_good

# System space and time definitions
dim 2
boundaries x 0 100
boundaries y 0 100
time_start 0
time_stop 500
time_step 0.05

# Molecular species and their properties
species L R M.1.0 M.1.1
difc L 3
difc R(up) 0.2
difc M.1.0 2
difc M.1.1 1.5
color L(all) green
color R(all) blue
color M.1.0(all) orange
color M.1.1(all) red
display_size all(all) 2

# BioNetGen parameters
start_bng lrm
multiply unimolecular_rate 1
multiply bimolecular_rate 1
#BNG2_path ../../../source/BioNetGen/BNG2.pl
monomer_state L fsoln
monomer_state R up
monomer_state M bsoln
expand_rules lrm.bngl
read_file lrm.net
end_bng

# Surface parameters
start_surface membrane
action both all(all) reflect
panel rect +1 0 50 100
end_surface

start_surface outsides
action both all(all) reflect
panel rect +x 0 0 100
panel rect -x 100 0 100
panel rect +y 0 0 100
panel rect -y 0 100 100
end_surface

# initial molecules
surface_mol 20 R(up) membrane all all
mol 20 L 50 80
mol 20 M.1.0 50 20

text_display time M.1.1 M* Rbound(all)

ifdefine OUTFILE
  output_files OUTFILE
  cmd a listmols OUTFILE
endif

end_file

