MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.
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.
Department of Chemistry, Stanford University, Stanford, California. Electronic address: rmcgibbo@stanford.edu.
Robert T
RT
McGibbon
Computational Biology Program, Sloan-Kettering Institute, New York, New York.
Kyle A
KA
Beauchamp
Department of Chemistry, Stanford University, Stanford, California.
Matthew P
MP
Harrigan
Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee.
Christoph
C
Klein
Department of Chemistry, Rutgers University, Piscataway, New Jersey.
Jason M
JM
Swails
Biophysics Program, Stanford University, Stanford, California.
Carlos X
CX
Hernández
Department of Chemistry, Stanford University, Stanford, California.
Christian R
CR
Schwantes
Department of Chemistry, University of California, Davis, Davis, California.
Lee-Ping
LP
Wang
SLAC National Accelerator Laboratory, Menlo Park, California.
Thomas J
TJ
Lane
Department of Chemistry, Stanford University, Stanford, California; Biophysics Program, Stanford University, Stanford, California.
Vijay S
VS
Pande
D020407:Internet; D056004:Molecular Dynamics Simulation; D012984:Software