2015
DOI: 10.1016/j.bpj.2015.08.015
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MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

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 roo… Show more

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Cited by 1,781 publications
(1,441 citation statements)
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“…88 Finally, the interactions are subsequently turned back on via a reverse of the original procedure.…”
Section: Theory and Computational Methodsmentioning
confidence: 99%
“…88 Finally, the interactions are subsequently turned back on via a reverse of the original procedure.…”
Section: Theory and Computational Methodsmentioning
confidence: 99%
“…We used MDTraj (version 1.7.2) 45 in combination with in-house Python scripts to calculate distances and dihedral angles.…”
Section: Methodsmentioning
confidence: 99%
“…We used the MDTraj 43 library to process individual structure and molecular dynamics coordinates in Python. 44 To select frames for a given shadow, we stored data in NumPy arrays and processed them using the NumPy library.…”
Section: Methodsmentioning
confidence: 99%