PT  - JOURNAL ARTICLE
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
TI  - MDTraj: a modern, open library for the analysis of molecular dynamics trajectories
AID  - 10.1101/008896
DP  - 2014 Jan 01
TA  - bioRxiv
PG  - 008896
4099  - http://biorxiv.org/content/early/2014/09/09/008896.short
4100  - http://biorxiv.org/content/early/2014/09/09/008896.full
AB  - 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.