MDRefine

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A package to perform refinement of MD simulation trajectories.
📚 Documentation is available at the project page.

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🚀 Installation

To install the package and dependencies from PyPI:

pip install MDRefine

To 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

📘 Getting Started

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.

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🧪 Continuous Integration

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).

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📚 References

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

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🙋‍♀️ Questions or Feedback?

Feel free to:

• Open an issue
• Contact the authors via email: igilardo@sissa.it