What is GROMACS
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids 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.
GROMACS is highly tuned for high performance computing environment. It supports various parallelization and acceleration schemes for different computing units.
Modules
To use GROMACS, please use the following commands or refer to the sample SLURM scripts:
| System | Version | Command |
|---|---|---|
| HPC2021 | 2021.3 | module load gromacs/2021.3 |
HPC2021 System
| Partition | MPI enabled | Thread-MPI enabled | GPU enabled | Executable |
|---|---|---|---|---|
| intel | Y | Y | gmx_mpi | |
| amd | Y | Y | gmx_mpi | |
| gpu | Y | Y | gmx |
Sample examples with SLURM script for running GROMACS in parallel are available at /share1/gromacs/sample.