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; eGFRD equilibrium simulation
;
; help
;
[Variables]
V = 40e-18 ; 40 femto liter = 40 atto m^3
ka = 1e-19 ; association constant in m^3*s^-1
kd = 2e-2 ; dissociation constant in s^-1
N = 100 ; number of particles A and B
; Calculate the analytic average number of C particles in equilibrium
kD = kd / ka
Nc_th = (2*N+kD*V - sqrt( (2*N+kD*V)^2 - 4*N*N)) / 2
[Simulator]
MaintenanceStep = 100000 ; check simulator internal consistency every N steps
MaintenanceFile = sim_dump.out ; dump full simulator state to file at maintenance cycle
[World]
Matrix = 8
Size = V^(1/3) ; volume in m^3 to cube-length in meter
[SpeciesType]
Name = A B C
r = 1e-9 ; m
D = 1e-12 ; m^2*s^-1
[ReactionRule]
Rule = A + B <=> C ; bidirectional bimolecular reaction rule
ka = ka
kd = kd
[Particles]
A = N ; insert A & B particles no C particles
B = N
C = 0
[CopyNumbers]
Interval = 1 ; output particle count every second
Type = Average