Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)
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
The documentation is available here.
Head over to the getting started tutorial.
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
git clone git@github.com:graeter-group/kimmdy-reactions.git
git clone git@github.com:graeter-group/kimmdy-grappa.git
cd kimmdy
python -m venv .venv
source ./venv/bin/activate
pip install -r requirements.txt
Conventions:
For developoment, we provide a docker image containing gromacs and multiple python versions to test against.
To run the test locally, you must:
gh extension install https://github.com/nektos/gh-actgh extension exec act -j test --artifact-server-path ./artifactsartifactsFAQs
Kinetic Monte Carlo Molecular Dynamics
We found that kimmdy demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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