MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

Naveen Michaud-Agrawal, Elizabeth J. Denning, Thomas B Woolf, Oliver Beckstein

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)2319-2327
Number of pages9
JournalJournal of Computational Chemistry
Volume32
Issue number10
DOIs
StatePublished - Jul 30 2011

Fingerprint

Molecular Dynamics Simulation
Molecular dynamics
Trajectories
Boidae
Trajectory
Amber
Computer simulation
Licensure
Libraries
Proteins
Python
Language
Databases
Linux
Protein Structure
Object-oriented
Protein
Atoms
Simulation

Keywords

  • analysis
  • membrane systems
  • molecular dynamics simulations
  • object-oriented design
  • proteins
  • Python programming language
  • software

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics
  • Medicine(all)

Cite this

MDAnalysis : A toolkit for the analysis of molecular dynamics simulations. / Michaud-Agrawal, Naveen; Denning, Elizabeth J.; Woolf, Thomas B; Beckstein, Oliver.

In: Journal of Computational Chemistry, Vol. 32, No. 10, 30.07.2011, p. 2319-2327.

Research output: Contribution to journalArticle

Michaud-Agrawal, Naveen ; Denning, Elizabeth J. ; Woolf, Thomas B ; Beckstein, Oliver. / MDAnalysis : A toolkit for the analysis of molecular dynamics simulations. In: Journal of Computational Chemistry. 2011 ; Vol. 32, No. 10. pp. 2319-2327.
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