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Supported Applications

MDAnalysis

  • Description

    an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.

  • Usage

    To list all executables provided by MDAnalysis, run: $ sbgrid-list mdanalysis Copy to clipboard

  • Usage Notes

    MDAnalysis is installed as a Python Module in Python version 2.7.12 on Linux and 2.7.5. on Mac. To use it, set a version override for the proper python version. There is info on how to do that here : https://sbgrid.org/wiki/versions

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install mdanalysis Copy to clipboard Available operating systems: Linux 64, OS X INTEL

  • Primary Citation*

    R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. 2016. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. Proceedings of the 15th Python in Science Conference (SCIPY 2016). 102-109.

    N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. 2011. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry. 32(10): 2319-2327.


    • *Full citation information available through

  • Citation Note

    Citations for included algorithms and modules can be found at: http://www.mdanalysis.org/docs/documentation_pages/references.html#references-components

  • Keywords

    Python Module

  • Default Versions

    Linux 64:  2.4.2 (910.2 MB)
    OS X INTEL:  2.4.2 (607.1 MB)

  • Other Versions

      Linux 64:

      2.1.0 (1.1 GB) , 2.2.0 (1.2 GB)

    • OS X INTEL:

      2.1.0 (960.7 MB) , 2.2.0 (1.1 GB)

  • Developers

    Beckstein Oliver, Michaud-Agrawal Naveen, Denning J Elizabeth, Woolf B Thomas, Reddy J. E. Tyler, Domański Jan, Linke Max, Gowers J Richard, Barnoud Jonathan, Melo N Manuel, Seyler L Sean, Dotson L David, Kenney M Ian, Buchoux Sébastien

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