Starting a Simulation With NERDSS

To start a new simulation, you need a parameter file with a .inp extension and all the required .mol files. The .mol files specify the structure of specific molecules, including the location of all interfaces, as well as translational and rotational diffusion constants. The .inp files control reaction rules and simulation settings. All input files can be automatically generated using the ionerdss package or the provided JAVA GUI.

Once you have all the necessary input files correctly formatted, you can run NERDSS using the following command:

./nerdss -f <your_param_file>

Ensure that all required .mol files referenced by the parameter file are in the same directory as the executable.

Here are some useful flags you can use with the nerdss command:

Flag	Description
-f <filename>, --parmfile <filename>	Specifies the parameter file (required).
-s <integer>, --seed <integer>	Manually sets a seed for the random number generator (optional).
-r <filename>, --restart <filename>	Specifies the restart file (required for restart simulation).
-a <filename>, --add <filename>	During a restart, reads updated and new parameters, adding to or overriding those in the original parameter file (optional).
--debug-force-dissoc	Forces dissociation to occur whenever possible (optional, for debugging only).
--debug-force-assoc	Forces association to occur whenever possible (optional, for debugging only).