# Michaelis-Menten reaction # units: micron and second graphics none dim 3 species E S ES P boxsize 0.3 # side length of each partition # diffusion coefficients difc E 10 difc S 10 difc ES 10 difc P 10 # simulation times time_start 0 time_stop 10 time_step 0.001 # system boundaries are periodic boundaries 0 0 4.4964 p boundaries 1 0 4.4964 p boundaries 2 0 4.4964 p # store molecules internally with separate list for each species molecule_lists Elist Slist ESlist Plist mol_list E Elist mol_list S Slist mol_list ES ESlist mol_list P Plist # initial molecule counts, uniformly distributed mol 909 E u u u # 10 E/vol mol 9091 S u u u # 100 S/vol # reactions and rates # fwd rate is 5.88 uM-1 s-1; binding radius is 0.0134 and would be 3.2e-5 if dt=0 reaction fwd E + S -> ES 0.01 reaction back ES -> E + S 1 reaction prod ES -> E + P 1 product_placement back pgemmax 0.2 # maximum probability of geminate recombination # save quantitative results output_files benchmarkout.txt cmd i 0 100 0.01 molcount benchmarkout.txt end_file