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Supported Applications

GROMACS

  • Description

    a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.

  • Usage Notes

    SBGrid Usage Info

    GROMACS is GPU-accelerated using Nvidia CUDA on Linux. For general information on running GPU accelerated applications from SBGrid, please see here : https://sbgrid.org/wiki/gpu

    CUDA builds of GROMACS are designated by a '_cu' suffix in the version of the application. For example, 2020.2_cu9.2.88 is linked against CUDA v9.2 libraries. All builds can be run on 'consumer-grade' GPU hardware.

    GROMACS builds which contain _plumed are compiles with PLUMED, https://www.plumed.org .

    2020.2_sse2_cu9.0 is compiled for older hardware (pre-intel Haswell CPUs, circa 2013)

    GROMACS and MPI versions

    GROMACS uses MPI and OpenMP for parallel processing. MPI is managed by the application and should not need to be explicity set in the shell. Please let us know if you have MPI problems or questions - bugs@sbgrid.org.

    Recent Changes

    20200703 : Add 2020.2_sse2_cu9.0 compatibility version

    Deprecated versions

    The following verions are deprecated and will be removed in a future SBGrid update, approximately one month from the date listed.

    20200706: 2019.1 2019.1_cu9.0 2019.5_cu9.2.88 2020.1 2020.1_cu9.2.88

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid install gromacs Copy to clipboard
  • Primary Citation*

    M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, and E. Lindahl. 2015. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 1: 19-25.
    (Note: Volume is actually 1-2.)


    • *Full citation information available through

  • Citation Note

    A full list of citations can also be found by visiting the GROMACS website.

  • Webinars

    Topic: Molecular Simulations with GROMACS: Possibilities and Pitfalls
    Presenter: Erik Lindahl, Professor, Stockholm University and KTH Royal Institute of Technology

    Date Recorded: May 28, 2015
    Host: Jason Key

  • Keywords

    Computational Chemistry

  • Default Versions

    Linux 64:  2020.2
    OS X INTEL:  2019.1

  • Other Versions

      Linux 64:

      2020.2_sse2_cu9.0, 2020.2_cu9.2.88, 2020.1_cu9.2.88, 2020.1, 2019.5_cu9.2.88, 2019.4_cu9.2.88_plumed, 2019.1_cu9.0, 2019.1
    • OS X INTEL:

      2018.2, 2018.1, 2018
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