GROMACS

GROMACS is a package to perform classical molecular dynamics simulations.

Installation on the clusters:

The GROMACS package can be run on any of the clusters. We provide the double precision version for both CPUs and GPUs built together with the PLUMED library. GROMACS benefits from optimizations targetted to specific CPUs, therefore apart from a generic build, we provide optimized binaries for Notchpeak Intel and AMD nodes. The binary is chosen automatically based on the CPU on which the module gets loaded. During our tests, the Notchpeak CPU optimized binaries provide about 80% performance increase over the generic binary.

The installations can be loaded as the following modules;

• generic CPU: module load gcc/8.5.0 intel-oneapi-mpi/2021.6.0 gromacs/2022.3
• Notchpeak Intel CPU: module load gcc/11.2.0 openmpi/4.1.4 gromacs/2022.3
• Notchpeak AMD CPU: module load gcc/11.2.0 openmpi/4.1.4 gromacs/2022.3
• generic GPU module load gcc/8.5.0  intel-oneapi-mpi/2021.6.0 gromacs/2022.3-gpu
• Notchpeak Intel CPU GPU module load gcc/11.2.0  openmpi/4.1.4 gromacs/2022.3-gpu

All executables are to be found in the "$GROMACS_ROOT/bin" directory. An example script is found in the /uufs/chpc.utah.edu/sys/installdir/gromacs/scripts directory, along with the input files used to test, in the scripts/example sub directory. 

Info on Gromacs  

The home page for Gromacs is http://www.gromacs.org/. At this site you will find a summary of the program's capabilities along with documentation on how to use the package.