kimmdy 5.1.9

Kinetic Monte Carlo Molecular Dynamics

KIMMDY

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

Installation

Note: Some reactions need a GROMACS version patched with PLUMED, gromacs name should then contain MODIFIED or plumed.

Bare Installation

git clone https://github.com/hits-mbm-dev/kimmdy.git
cd kimmdy
python -m venv .venv
source .venv/bin/activate
python -m pip install -e ./

This installation includes only the most basic functionality as no plugins and analysis tool dependencies are installed. Plugins can be installed using python -m pip install -e ./ in their module directories (e.g. kimmdy/plugins/default_reactions). The analysis tool dependencies can be installed with python -m pip install -e ./[analysis] in kimmdy/.

Full installation

conda create -n kimmdy_full python=3.10 tensorflow==2.10 openmm
conda activate kimmdy_full
git clone https://github.com/hits-mbm-dev/HAT_reaction_plugin.git
cd HAT_reaction_plugin/
pip install -r requirements.txt
cd ..
git clone https://github.com/hits-mbm-dev/grappa.git
cd grappa
pip install -e .
cd ..
git clone https://github.com/hits-mbm-dev/kimmdy.git
cd kimmdy
pip install -r requirements.txt
pip install -e ./[parameterization_plugins]

Other ways to install kimmdy with all plugins are currently discouraged because of the high number of dependencies.

Documentation

GitHub pages

GitHub Pages documentation

Local documentation

cd <kimmdy root directory>
pip install -r requirements.txt # Documentation depends on packages in requirements.txt
make docs
quarto preview # Should open the documentation in your standard browser

Development setup

• install packages necessary for developmentmake python -m pip install -r requirements.txt
• code style: black
• docstrings: numpy
• Conventional commit messages when possible for pretty release notes.

First simulation

• change directory to example_triala
• run kimmdy: kimmdy -l INFO
• check output: kimmdy.log, test_out_00X/

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