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Biophys J. 2015 Oct 20;109(8):1528-32. doi: 10.1016/j.bpj.2015.08.015.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

Author information

1
Department of Chemistry, Stanford University, Stanford, California. Electronic address: rmcgibbo@stanford.edu.
2
Computational Biology Program, Sloan-Kettering Institute, New York, New York.
3
Department of Chemistry, Stanford University, Stanford, California.
4
Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee.
5
Department of Chemistry, Rutgers University, Piscataway, New Jersey.
6
Biophysics Program, Stanford University, Stanford, California.
7
Department of Chemistry, University of California, Davis, Davis, California.
8
SLAC National Accelerator Laboratory, Menlo Park, California.
9
Department of Chemistry, Stanford University, Stanford, California; Biophysics Program, Stanford University, Stanford, California.

Abstract

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, 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 MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python.

PMID:
26488642
PMCID:
PMC4623899
DOI:
10.1016/j.bpj.2015.08.015
[Indexed for MEDLINE]
Free PMC Article

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