GROMACS#
GROMACS is a versatile package for molecular dynamics simulation. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
CUDA-based GPU acceleration is available for Since GROMACS >= 4.6, for Nvidia compute capability >= 2.0 GPUs (e.g. Fermi or later).
On Bede, GROMACS is made available through the HECBioSim Project.
# Load the hecbiosim project
module load hecbiosim
# Load the desired version of gromacs
module load gromacs/2020.4-plumed-2.6.2-rhel8
module load gromacs/2021.1-plumed-2.7.2-rhel8
module load gromacs/2021.2-plumed-2.7.1-rhel8
module load gromacs/2021.2-plumed-2.7.2-rhel8
module load gromacs/2021.4-plumed-2.7.3-rhel8
module load gromacs/2021.5-rhel8
module load gromacs/2022.0-rhel8
module load gromacs/2022.2
module load gromacs/2023.1
The HECBioSim project also provide example bede job submission scripts for GROMACS on their website.
For more information see the GROMACS documentation and information on GPU acceleration within GROMACS.