aimmd-lab

AIMMD-Lab

This repository implements AI for Molecular Mechanism Discovery (AIMMD) — AI-enhanced path sampling for rare molecular transitions.

AIMMD generates short unbiased simulations from configurations chosen by a machine-learned committor model, building a diverse ensemble of trajectories that approximates a long equilibrirum trajecotory at a fraction of the computational cost. That ensemble is reweighted to recover free-energy profiles and transition rates, while the learned committor doubles as an interpretable reaction coordinate. Runs scale from a laptop (multiprocessing) to HPC clusters (SLURM srun), driving the GROMACS MD engine or a built-in toy engine.

📖 Documentation: https://aimmd-lab.readthedocs.io

A alternative package implementing AIMMD as published in Jung et al. (2023) is available at https://github.com/bio-phys/aimmd.

Features

• Committor-guided two-way shooting in the reactive region.
• Rejection-free path sampling (rfps) and classic TPS acceptance (tps).
• On-the-fly training and reweighting — the committor model, adaptive bins, and densities update continuously as data arrives.
• Free energies and rates from a single self-consistent path ensemble.
• Multi-system / multi-ligand runs trained with one shared committor network.
• Biased dynamics (OPES/PLUMED) with Tiwary–Parrinello rate reweighting.
• Graph-neural-network committor models (optional).
• Local or HPC execution from the same parameter file.

Installation

From PyPI

pip install aimmd-lab

The distribution is named aimmd-lab, but the import name is aimmd:

import aimmd

We recommend a clean conda environment (Python 3.13 is tested):

conda create -n aimmd python=3.13
conda activate aimmd
pip install aimmd-lab

Prerequisites: GROMACS

AIMMD drives the GROMACS MD engine and expects gmx or gmx_mpi on your PATH. For testing and lightweight work it can be installed from conda-forge:

conda install conda-forge::gromacs

For production runs we recommend building GROMACS from source for optimal performance; see the GROMACS install guide. (The built-in toy engine needs no GROMACS.)

Optional: graph neural networks

Graph-based committor models need extra packages (torch-cluster can be awkward to build). Install the graphs extra plus mlcolvar:

pip install "aimmd-lab[graphs]"
pip install mlcolvar

If the default wheels do not match your CUDA/Python build, install them explicitly — see the installation guide for a confirmed-working CUDA 11.8 / Python 3.13 example.

Development install

git clone https://github.com/covinolab/AIMMD-Lab.git
cd AIMMD-Lab
pip install -e ".[tests,docs]"
pytest tests/          # verify the installation

Quickstart

An AIMMD run is defined by a params.py file (states, features, network, engine, sampling controls) and a short launch script:

import aimmd

params   = aimmd.Params.load('params.py')   # load the run configuration
launcher = aimmd.Launcher(params, 'run1')   # attach a working directory

# 5 shooting workers, 1 free-A, 1 free-B; stop after 25k frames.
launcher.run(5, 1, 1, nframes=25000)

# Reload and analyze the resulting path ensemble.
ensemble = params.pathensemble('run1')
ensemble.report()
ensemble.reweight()      # free energies / rates

See the Quickstart and the runnable tutorial notebooks (a 1-D toy system and a multi-ligand run, both GROMACS-free) for complete examples.

Documentation

Full documentation is hosted at https://aimmd-lab.readthedocs.io, including:

• Concepts and the scientific background,
• the workflow and advanced usage (multi-system, biased dynamics, validation),
• the full parameter reference and API reference.

Citation

If you use AIMMD in your work, please cite the relevant papers:

1. Jung, H.; Covino, R.; Arjun, A.; Leitold, C.; Dellago, C.; Bolhuis, P. G.; Hummer, G. Machine-Guided Path Sampling to Discover Mechanisms of Molecular Self-Organization. Nat. Comput. Sci. 2023, 3 (4), 334–345. https://doi.org/10.1038/s43588-023-00428-z
2. Lazzeri, G.; Jung, H.; Bolhuis, P. G.; Covino, R. Molecular Free Energies, Rates, and Mechanisms from Data-Efficient Path Sampling Simulations. J. Chem. Theory Comput. 2023, 19 (24), 9060–9076. https://doi.org/10.1021/acs.jctc.3c00821
3. Lazzeri, G.; Bolhuis, P. G.; Covino, R. Optimal Rejection-Free Path Sampling. arXiv 2025. https://arxiv.org/abs/2503.21037

A CITATION.cff file is included for GitHub's "Cite this repository" feature.

Contributing

Contributions are welcome — see CONTRIBUTING.md and the developer guide.

License

AIMMD is released under the MIT License. See LICENSE.