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 do not need to be patched with plumed, only the PLUMED_KERNEL variabel needs to be set. (See plumded documentation)

Installation

uv tool install -p 3.11 kimmdy[plugins]

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

plugins can be also more specific, like hat, hydrolysis, grappa, dimerization, or reactions (containing homolysis, hat_naive and a dummyreaction).

Notes on the project strucure

Plugins are developed in separate git repositories. Officially supported ones 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