Structure of the NERDSS Input Files

NERDSS requires two input files to simulate a model: a parameter file (parms.inp) and a molecule structure file for each species in the system (SPECIES1.mol, SPECIES2.mol, etc.).

INP Files: The main input file for NERDSS that includes simulation parameters.

• Includes: timesteps, dimensions, included molecules, and reactions.

MOL Files: Each file stores information about each included molecule.

• Includes: name, diffusion constants, Center of Mass, binding sites.

For more information, refer to the NERDSS User Guide.