MDAnalysis

MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.

MDAnalysis allows one to read particle-based trajectories (including individual coordinate frames such as biomolecules in the PDB format) and access the atomic coordinates through NumPy arrays. This provides a flexible and relatively fast framework for complex analysis tasks. In addition, powerful atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out. The basic example demonstrates some of these features.

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Availability

MDAnalysis can be easily installed with its dependencies using the pip or conda package managers; MDAnalysis is also available in some recent Linux distributions.

All source code is available under the GNU General Public License, version 2 (or any later version at your choice) from github.com/MDAnalysis/mdanalysis and the Python Package index pypi.org/project/MDAnalysis.

Participating

Ask questions on the GitHub Discussions mailing list and be part of the conversation. You can also join the MDAnalysis Discord Server to talk with other users and developers. (In order to join our Discord server, use the invitation link https://discord.gg/fXTSfDJyxE.)

Please report bugs or enhancement requests through the Issue Tracker.

MDAnalysis is open source and welcomes your contributions. Fork the repository on GitHub and submit a pull request. Participate on the GitHub Discussions (Development) mailing list.

MDAnalysis regularly takes part in various mentoring and outreach programs, such as Google Summer of Code, Google Season of Docs, Outreachy, the Station1 Frontiers Fellowship, and the CompChemURG mentorship schemes. Many of the current core developers joined the project through these mentoring schemes. The project also frequently offers teaching workshops, both online and in-person. Follow our blog, Twitter, and LinkedIn pages for updates on how to participate.

Supporting

If you like MDAnalysis and want to support our mission, please consider making a donation to support our efforts.

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(Donations are made through our fiscal sponsor, NumFOCUS, which is a 501(c)(3) non-profit charity in the United States; as such, donations to NumFOCUS are tax-deductible as allowed by law. As with any donation, you should consult with your personal tax adviser or the IRS about your particular tax situation.)

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