# Single molecule tracking test

random_seed 1

graphics opengl_good
dim 2

boundaries 0 0 20 r
boundaries 1 0 20 r

time_start 0
time_stop 100
time_step 0.001

species receptor ligand bound

difc ligand 1

color receptor red
color ligand green
color bound yellow
display_size all(all) 0.3

reaction rxn1 receptor + ligand -> bound 3
reaction_serialnum rxn1 r2
ifdefine OUTFILE
  reaction_log OUTFILE rxn1 1
else
  reaction_log stdout rxn1 1
endif

reaction rxn2 bound -> receptor + ligand 1
reaction_serialnum rxn2 new + r1
reaction_log OUTFILE rxn2 1

mol 1 ligand u u
mol 50 receptor u u

ifdefine OUTFILE
  output_files OUTFILE
  cmd N 100 trackmol 1 OUTFILE
  cmd a listmols OUTFILE
else
  cmd B echo stdout "listmols:\n"
  cmd B listmols stdout
  cmd N 100 trackmol 1 stdout
endif

end_file

