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

Biophysical Journal · 2015 · Vol. 109(8) · pp. 1528–1532

Robert T. McGibbon✉(Stanford Medicine)Kyle A. Beauchamp(Kettering University)Matthew P. Harrigan(Stanford University)Christoph Klein(Vanderbilt University)Jason Swails(Rutgers, The State University of New Jersey)Carlos X. Hernández(Stanford University)Christian R. Schwantes(Stanford University)Lee‐Ping Wang(University of California, Davis)Thomas J. Lane(SLAC National Accelerator Laboratory)Vijay S. Pande(Stanford University)

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Mass Spectrometry Techniques and Applications Protein Structure and Dynamics RNA and protein synthesis mechanismsPython (programming language)Computer scienceInteroperabilitySoftwareVisualizationData structureComputational scienceData miningSoftware engineeringData science

MeSH terms

SoftwareInternetMolecular Dynamics Simulation

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2,473

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References

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

Journal of Chemical Theory and Computation · 2008 · 15,846 citations

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

Journal of Chemical Theory and Computation · 2012 · 745 citations

Fast Parallel Algorithms for Short-Range Molecular Dynamics

Journal of Computational Physics · 1995 · 43,820 citations

General purpose molecular dynamics simulations fully implemented on graphics processing units

Journal of Computational Physics · 2008 · 1,497 citations

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

Journal of Chemical Theory and Computation · 2009 · 945 citations

Scalable molecular dynamics with NAMD

Journal of Computational Chemistry · 2005 · 17,211 citations

<scp>CHARMM</scp>: A program for macromolecular energy, minimization, and dynamics calculations

Journal of Computational Chemistry · 1983 · 14,885 citations

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

Journal of Computational Chemistry · 2011 · 4,288 citations

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