# Simple crowded system simulation.  This file was used to create Figure 3E,F
# in Andrews, 2016.
# Values are roughly right for hemoglobin
# Units are nm and us

define SEED 1
define NMOL 6112	# 40% volume occupancy
define HGRADIUS 2.5
#define BETTERGRAPHICS

ifdefine BETTERGRAPHICS
  graphics opengl_better
  light room ambient 0 0 0
  light 0 position -1 1 1 0
  light 0 diffuse 0.5 0.5 0.5
  light 0 ambient 0.5 0.5 0.5
  light 0 specular 0.5 0.5 0.5
else
  graphics opengl
  graphic_iter 1000
endif

#random_seed SEED

dim 3
boundaries x 0 100 p
boundaries y 0 100 p
boundaries z 0 100 p

species Hg

difc Hg 65

color Hg lightred
display_size Hg HGRADIUS

time_start 0
time_stop 6.1
time_step 0.0001

frame_thickness 2

mol NMOL Hg u u u

reaction r1 Hg + Hg -> Hg + Hg
binding_radius r1 2*HGRADIUS
product_placement r1 bounce

output_files crowdingout.txt crowdingmsdout.txt
output_format csv
cmd i 1 20 0.5 radialdistribution Hg Hg 20 100 10 crowdingout.txt
cmd i 1 20 0.5 meansqrdisp Hg all crowdingmsdout.txt

end_file