gmxapi Python package

Version 0.5.0a1.

gmxapi allows molecular simulation and analysis work to be staged and run from Python.

After installing GROMACS and the gmxapi Python package, you can use pydoc gmxapi from the command line or import gmxapi; help(gmxapi) within a Python interpreter for concise usage help. Complete documentation is collected in the following sections.

• 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

To discuss gmxapi, use the #gmxapi tag on the GROMACS user discussion forum. Report bugs through the GROMACS issue tracker.

Complete documentation for the gmxapi Python package is part of the GROMACS manual since gmxapi version 0.1. Older releases can also be found at GitHub. Pre-release documentation may be found at https://manual.gromacs.org/nightly/gmxapi/.

See also

gmxapi publications

Irrgang, M. E., Davis, C., & Kasson, P. M. gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support. PLOS Comput Biol 2022. DOI: 10.1371/journal.pcbi.1009835

Irrgang, M. E., Hays, J. M., & Kasson, P. M. gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations. Bioinformatics 2018. DOI: 10.1093/bioinformatics/bty484