MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

MDAnalysis is an object‐oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance‐critical code in C. It uses the powerful NumPy package to expose trajectory d...

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Bibliographic Details
Published in:Journal of computational chemistry Vol. 32; no. 10; pp. 2319 - 2327
Main Authors: Michaud-Agrawal, Naveen, Denning, Elizabeth J., Woolf, Thomas B., Beckstein, Oliver
Format: Journal Article
Language:English
Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 30.07.2011
Wiley Subscription Services, Inc
Subjects:
analysis
Computational Biology
membrane systems
Molecular Dynamics Simulation
molecular dynamics simulations
Molecular structure
object-oriented design
Programmers
Programming languages
Proteins
Python programming language
Simulation
Software
Software packages
Syntax
UNIX
molecular dynamics simulations
software
object-oriented design
proteins
membrane systems
analysis
Python programming language
ISSN:0192-8651, 1096-987X, 1096-987X
Online Access:Get full text
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Summary:MDAnalysis is an object‐oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance‐critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix‐based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com. © 2011 Wiley Periodicals, Inc. J Comput Chem 2011
Bibliography:ArticleID:JCC21787
istex:BE718293D4E3218886CE84BB21F3019960EA7901
Burroughs Wellcome Fund
Junior Research Fellowship at Merton College, Oxford
ark:/67375/WNG-FF7PBZ00-L
National Institutes of Health - No. GM064746
European Union (EDICT Project) - No. 201924
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ISSN:0192-8651
1096-987X
1096-987X
DOI:10.1002/jcc.21787