MDAnalysisData: MD data for testing, learning, and benchmarking

Zenodo DOI PRs welcome tests test coverage




Jul 07, 2024

MDAnalysisData is a collection of datasets from the field of computational biophysics, with an emphasis on trajectories from molecular dynamics (MD) simulations and the structure and dynamics of biomolecules.

Data sets are stored at external stable URLs (e.g., on figshare , zenodo, or DataDryad) and not inside the MDAnalysisData package. Instead, the MDAnalysisData.datasets provides a simple interface to download, cache, and access these externally hosted data sets.

The files can be easily used with MDAnalysis but the package is standalone and can be used for any purpose, for instance, to provide examples for workshops and classes, and, of course, to try out other tools for analyzing simulations.

Datasets are released under an open license that conforms to the Open Definition 2.1 that allows free use, re-use, redistribution, modification, separation, for any purpose and without a charge. All code can be found in the public GitHub repository mdanalysis/MDAnalysisData.

This library is under active development. We use semantic versioning to indicate clearly what kind of changes you may expect between releases. Please raise any issues or questions in the Issue Tracker. Contributions of data sets and code in the form of pull requests are very welcome.