; eGFRD bimolecular reaction simulation ; units are nm and us [Variables] V = 8000000 ; volume in nm^3 [Simulator] MaintenanceStep = 10000 ; check simulator internal consistency every N steps MaintenanceFile = sim_dump.out ; dump full simulator state to file at maintenance cycle EndTime = 200 [World] Matrix = 8 Size = V^(1/3) ; volume is in nm^3 [SpeciesType] Name = A B C r = 0.4 ; diffusion-limited radii: 0.0199 for k=1, 0.199 for k=10 and 1.99 for k=100. D = 1 ; nm^2*us^-1 [ReactionRule] Rule = A + B -> C ; bimolecular reaction rule k = 10 ; 10 nm^3/us [Particles] A = 8000 ; insert particles B = 8000 C = 0 [CopyNumbers] Interval = 0.1 ; output particle count Type = Instantaneous ;File = bireact_m.dat