A package to perform refinement of MD simulation trajectories.
📚 Documentation is available at the project page.
To install the package and dependencies from PyPI:
pip install MDRefineTo install the development version from source:
git clone https://github.com/bussilab/MDRefine.git
cd MDRefine
pip install -e .
We recommend installing in a dedicated environment to avoid polluting your base Python setup:
python3 -m venv env
source env/bin/activate
pip install MDRefine
To activate this environment in a new terminal:
source /path/to/env/bin/activate
We suggest running the tutorials in the Examples/ folder to gain insights into MDRefine's usage for:
- Refinement of molecular ensembles
- Force field correction
- Forward model optimization
The Examples/ include Jupyter notebooks and scripts demonstrating practical workflows.
This repository uses GitHub Actions for automatic testing across Python versions and operating systems.
CI runs are skipped for documentation-only commits (e.g., README.md changes).
MDRefine builds on recent advances in ensemble refinement. If you use this package, please cite:
- Gilardoni, I., Piomponi, V., Fröhlking, T., & Bussi, G. (2025).
MDRefine: A Python package for refining molecular dynamics trajectories with experimental data.
The Journal of Chemical Physics, 162(19).
https://doi.org/10.1063/5.0256841
Feel free to:
- Open an issue
- Contact the authors via email:
igilardo@sissa.it