Table 2.

A description of each command line argument and their default values

Command line parameter	Description	Which methods use it	Default value
Filename	NetCDF file name	All	None
Random Seed	The random number generator's seed value.	All	Randomized (system dependent)
Epsilon (ε)	Minimum number of molecules of both reactant & product species for approximation to a continuous Markov process	All HyJCMSS simulation methods	100 molecules
Lambda (λ)	Minimum rate of reaction for approximation to a continuous Markov process	All HyJCMSS simulation methods	10 molecules/sec
MSR Tolerance	Maximum relative effect of slow reactions per numerical integration of SDEs	All HyJCMSS simulation methods	1/ε
SDE Tolerance	Maximum values of drift& diffusion error criteria	Adaptive Methods	1e-4
SDE time step	Maximum time step of numerical integrator	Fixed Methods	0.10 seconds or Save Time