Common Issues

Submodules

Clone with added --recurse-submodules.
Update submodules with git submodule update --init --recursive.
See Project Structure.

Plumed

Plumed is required for the homolysis plugin. Historically, gromacs would need to be compiled with Plumed, however since gromacs 2025, no patching is required. Plumed needs still to get compiled and installed (See plumded documentation)! Make sure the PLUMED_KERNEL env variable is set to the path to your libplumedKernel.so (should be in plumed/lib/).

What plugins do exist?

Check the kimmdy github topic to find them all.

uv related issues

For the tool installation, try uninstalling and re-installing.

For the dev installation, here are the most useful commands you might need:

Update dependencies to pyproject.toml content, run from kimmdy directory:

uv sync --extra all

Use a known set of dependency versions from uv.lock: (For downgrading pull an older uv.lock from github)

uv run --frozen kimmdy