# modifications.txt
# Example file to illustrate MZR modifications

graphics opengl_good

rand_seed 1
dim 2
max_species 100
max_mol 1000

species A

difc all 20.0

color A 1 0 0		# red

time_start 0
time_stop 5
time_step 0.01

boundaries 0 0 100 r
boundaries 1 0 100 r

start_rules
==== Modifications ====
  name=None, mass=0;
  name=Phos, mass=95;

==== Molecules ====
  A(*Site1 {None,Phos}, *Site2 {None,Phos}, *Site3 {None,Phos}), mass = 10000;

==== Transformation-Reactions ====
  A(*Site1{None}) -> A(*Site1{Phos}), k=1;
  A(*Site2{None}) -> A(*Site2{Phos}), k=1;
  A(*Site3{None}) -> A(*Site3{Phos}), k=1;
  A(*Site1{Phos}) -> A(*Site1{None}), k=1;
  A(*Site2{Phos}) -> A(*Site2{None}), k=1;
  A(*Site3{Phos}) -> A(*Site3{None}), k=1;

end_rules

mol 250 A u u

output_files stdout
cmd N 10 molcount stdout
cmd A molcountheader stdout

end_file