Introduction

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.

Publications

  1. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.
    Cite this
    Michaud-Agrawal N, Denning EJ, Woolf TB, Beckstein O, 2011-07-01 - Journal of computational chemistry

Credits

  1. Naveen Michaud-Agrawal
    Developer

    Department of Biophysics, Johns Hopkins School of Medicine

  2. Elizabeth J Denning
    Developer

  3. Thomas B Woolf
    Developer

  4. Oliver Beckstein
    Investigator

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Summary
AccessionBT002163
Tool TypeApplication
Category
Platforms
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Submitted ByOliver Beckstein