a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.
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 - firstname.lastname@example.org.
20200703 : Add 2020.2_sse2_cu9.0 compatibility version
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
InstallationUse the following command to install this title with the CLI client:
$ sbgrid-cli install gromacs
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 NoteA full list of citations can also be found by visiting the GROMACS website.
OS X INTEL:2018.2, 2018.1, 2018
Berk Hess, David Van der Spoel, Erik Lindahl