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bioRxiv · 10.1101/008896

MDTraj: a modern, open library for the analysis of molecular dynamics trajectories

Robert T McGibbon·Kyle A Beauchamp·Christian R Schwantes·Lee-Ping Wang·Carlos X Hernández·Matthew P Harrigan·Thomas J Lane·Jason M Swails·Vijay S Pande
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Abstract

Summary: MDTraj is a modern, lightweight and efficient software package for analyzing molecular dynamics simulations. MDTraj reads trajectory data from a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including RMSD, DSSP secondary structure assignment and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between molecular dynamics data and the rapidly-growing collection of industry-standard statistical analysis and visualization tools in Python. Availability: Package downloads, detailed examples and full documentation are available at http://mdtraj.org. The source code is distributed under the GNU Lesser General Public License at https://github.com/simtk/mdtraj.

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Robert T McGibbon, Kyle A Beauchamp, Christian R Schwantes, Lee-Ping Wang, Carlos X Hernández, Matthew P Harrigan, Thomas J Lane, Jason M Swails, Vijay S Pande. 2014-09-09. MDTraj: a modern, open library for the analysis of molecular dynamics trajectories. https://doi.org/10.1101/008896

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