Install KIMMDY with Plugins

Author

Kai Riedmiller

Complete Installation with ML Plugins

Prerequisites

  • uv: recommended package manager to install kimmdy. Get it here
  • gromacs>=2023.2
    • Version 2021.4 works with everything except slow-growth.

Optional:

  • plumed-patched version of gromacs (for the homolysis reaction). Gromacs 2025 and above does not need to be patched with plumed, only the PLUMED_KERNEL variabel needs to be set to your lib/libplumedKernel.so. (See plumded documentation)

Installation

uv tool install -p 3.11 kimmdy[all]

kimmdy, its subcommands, and its plugins are now availabe, test it with:

kimmdy --help

Uninstall by using:

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

To run kimmdy, either activate the venv:

source .venv/bin/activate
kimmdy --help

.. or use uv run:

uv run kimmdy --help

Instead of installing all plugins, 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

Notes on the project strucure

Plugins are developed in separate git repositories. Check the kimmdy github topic to find them all.

Officially supported plugins are linked as subrepositories of kimmdy inside the plugins directory. These are by default not pulled via git clone, to clone them add --recurse-submodules.

To update them, get new ones, or pull them after initially omitting them, use:

git submodule update --init --recursive
Back to top