KIMMDY

Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)

Installation

Note: KIMMDY requires GROMACS to be installed. Some reactions need a GROMACS version patched with PLUMED. The gromacs version name should then contain MODIFIED or plumed.

While it is possible to install KIMMDY with just pip install kimmdy, this can take a while due to dependency resolution. We recommend installing KIMMDY with uv instead:

uv tool install -p 3.11 kimmdy

This installation includes only the most basic functionality as no plugins and analysis tools are installed.

To install the builtin reaction plugins, use

uv tool install -p 3.11 kimmdy[plugins]

To install the builtin example reactions and analysis tools use

uv tool install -p 3.11 kimmdy[reactions,analysis]

However, this is only half the fun!

To install KIMMDY with all currently available official plugins, like kimmdy-grappa, which properly parameterizes your molecules for radicals using GrAPPa (Graph Attentional Protein Parametrization) and reaction plugins like kimmdy-hat (for Hydrogen Atom Transfer) or kimmdy-hydrolysis use

uv tool install -p 3.11 kimmdy[plugins]

To uninstall KIMMDY again, use

uv tool uninstall kimmdy

Documentation

The documentation is available here.

Getting started

Head over to the getting started tutorial.

Development

Development setup

Clone kimmdy and the default reaction and parameterization plugins and install requirements and kimmdy as editable via

git clone git@github.com:graeter-group/kimmdy.git --recurse-submodules
cd kimmdy
uv sync --extra plugins

Conventions:

  • code style: black
  • docstrings: numpy
  • Conventional commit messages when possible for pretty release notes.

Local testing

For developoment, we provide a docker image containing gromacs and multiple python versions to test against.
To run the test locally, you must:

  • install docker
  • install act, the easiest option is with github cli via gh extension install https://github.com/nektos/gh-act
  • run tests with gh extension exec act -j test --artifact-server-path ./artifacts
  • html coverage report is exported into artifacts
Back to top