KIMMDY

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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.

pip install kimmdy

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

To install the builtin reaction plugins, use

pip install kimmdy[reactions]

To install the builtin reactions and analysis tools use

pip install kimmdy[reactions,analysis]

However, this is only half the fun!

KIMMDY has two exciting plugins in the making, which properly parameterize your molecules for radicals using GrAPPa (Graph Attentional Protein Parametrization) and predict Hydrogen Atom Transfer (HAT) rates. Full installation instructions are available here

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:hits-mbm-dev/kimmdy.git
git clone git@github.com:hits-mbm-dev/kimmdy-reactions.git
git clone git@github.com:hits-mbm-dev/kimmdy-grappa.git
cd kimmdy
python -m venv .venv
source ./venv/bin/activate
pip install -r requirements.txt

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
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