@article {McGibbon008896, author = {Robert T. McGibbon and Kyle A. Beauchamp and Christian R. Schwantes and Lee-Ping Wang and Carlos X. Hern{\'a}ndez and Matthew P. Herrigan and Thomas J. Lane and Jason M. Swails and Vijay S. Pande}, title = {MDTraj: a modern, open library for the analysis of molecular dynamics trajectories}, elocation-id = {008896}, year = {2014}, doi = {10.1101/008896}, publisher = {Cold Spring Harbor Laboratory}, 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.}, URL = {https://www.biorxiv.org/content/early/2014/09/09/008896}, eprint = {https://www.biorxiv.org/content/early/2014/09/09/008896.full.pdf}, journal = {bioRxiv} }