TY - JOUR T1 - MDTraj: a modern, open library for the analysis of molecular dynamics trajectories JF - bioRxiv DO - 10.1101/008896 SP - 008896 AU - Robert T. McGibbon AU - Kyle A. Beauchamp AU - Christian R. Schwantes AU - Lee-Ping Wang AU - Carlos X. Hernández AU - Matthew P. Herrigan AU - Thomas J. Lane AU - Jason M. Swails AU - Vijay S. Pande Y1 - 2014/01/01 UR - http://biorxiv.org/content/early/2014/09/09/008896.abstract N2 - 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. ER -