# Smoldyn configuration file for MinD dimerization and nucleotide dynamics
# Units are microns and seconds

define ATPC	930000
define ADPC	116000

define KAD	(0.37e-6)*ADPC
define KDA	0.05
define KAT	(1.1e-6)*ATPC
define KTA	0.05
define KDT	(1.1e-6)*ATPC
define KTD	(0.37e-6)*ADPC
define KDIMER	8.5e-4
define KDISS	1
define KHYDRO	1.2e-3

# Graphical output
graphics opengl
graphic_iter 100

# System space and time definitions
dim 3
boundaries x 0 1 p
boundaries y 0 1 p
boundaries z 0 1 p

time_start 0
time_stop 30
time_step 0.001

# Molecular species and their properties
species A D T

difc all 2.6
color A blue
color D green
color T red

display_size all 2

# Reactions
reaction_rule rxnAtoD	*A* <-> *D*	KAD KDA
reaction_rule rxnAtoT	*A* <-> *T*	KAT KTA
reaction_rule rxnDtoT	*D* <-> *T*	KDT KTD
reaction_rule rxndimer	T + T -> TT	KDIMER
reaction_rule rxndissoc	?? -> ? + ?	KDISS
reaction_rule rxnhydro	?&T -> ?&D	KHYDRO

#expand_rules on-the-fly
expand_rules all

# initial molecules
mol 2000 A u u u

output_files MinDdimerout.txt
output_format CSV
cmd B molcountheader MinDdimerout.txt
cmd i 10 30 1 molcount MinDdimerout.txt

end_file