Advertisement

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

Authors

  • Naveen Michaud-Agrawal,

    1. Department of Biophysics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
    Search for more papers by this author
  • Elizabeth J. Denning,

    1. Department of Biophysics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
    2. Department of Pharmaceutical Chemistry, University of Maryland, Baltimore, School of Pharmacy, Baltimore, Maryland 21201
    Search for more papers by this author
  • Thomas B. Woolf,

    Corresponding author
    1. Department of Biophysics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
    2. Department of Physiology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
    • Department of Biophysics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
    Search for more papers by this author
  • Oliver Beckstein

    Corresponding author
    1. Department of Physiology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
    2. Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
    • Department of Physiology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
    Search for more papers by this author

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 http://mdanalysis.googlecode.com. © 2011 Wiley Periodicals, Inc. J Comput Chem 2011

Ancillary