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[all]

This installation includes all official reaction plugins and analysis tools.

To install only the most basic functionality, run:

uv tool install -p 3.11 kimmdy

You can also pick the plugins you want, the available extras are:

• reactions: makes homolysis, hat-naive and dummyreaction reactions available.
• grappa: allows parametrization of any system on-the-fly.
• hat: hydrogen atom transfer reaction plugin
• hydrolysis: hydrolysis reaction plugin
• dimerization: dimerization reaction plugin

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, the default reaction and parameterization plugins, then install kimmdy as editable module via

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

To load or update the submodules, run:

git submodule update --init --recursive

Run kimmdy either using uv run kimmdy, or activate the virtual environment uv has created:

source .venv/bin/activate
kimmdy --help

Conventions:

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

For more information, head to the documentation