SysSynBio / NERDSS

NonEquilibrium Reaction-Diffusion Self-assembly Simulator

NERDSS

Structure-Resolved Reaction-Diffusion Simulation Software by Johnson Lab, JHU

Installation

To build NERDSS, you need:

1. A C++ compiler:
   • For macOS, install XCode
   • For Ubuntu, install a compiler through apt
2. GNU Scientific Library (GSL) version 1.0 or higher:
   • For macOS, install via Homebrew
   • For Ubuntu, install via apt
3. To compile using make:
   • Navigate to the main directory
   • Run make serial
   • The executable will be placed in the ./bin directory

Running Simulations

1. Example input files are located in the subdirectories within the sample_inputs folder. They can also be generated using the python GUI program, which is also included in the ioNERDSS tool.

2. To start the simulation, use the command ./nerdss -f parms.inp.

Analyzing Results

1. Use the ioNERDSS PyPi library for visualizing simulation results.
2. Install ioNERDSS with pip install ioNERDSS.
3. Refer to the ioNERDSS repository for more details.