Python User Guide

• Full installation instructions
  • Overview
  • Background
  • Installing the Python package
  • Accessing gmxapi documentation
  • Testing
  • Troubleshooting
• Using the Python package
  • Notes on parallelism and MPI
  • Running simple simulations
  • Running ensemble simulations
  • Input arguments and “ensemble” syntax
  • Accessing command line tools
  • Preparing simulations
  • Using arbitrary Python functions
  • Subgraphs
  • Looping
  • Logging
  • More
• gmxapi Python module reference
  • Interface concepts
  • gmxapi basic package
  • Simulation module
  • Utilities
  • Status messages and Logging
  • Exceptions module
  • gmx.version module
  • Core API

After installing GROMACS and the gmxapi Python package, use pydoc gmxapi from the command line or import gmxapi; help(gmxapi) within Python for package and module documentation.