GROMACS version 2021.5 is installed and available for use on the HPC.
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, 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.
GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation.
GROMACS Quickstart Command Line Guide¶
When running on a single node (–ntasks=1 in SLURM )
gmx make_ndx <OPTIONS>
gmx grompp <OPTIONS>
gmx mdrun <OPTIONS>
When running on more than one node (–ntasks>1 in SLURM)
mpirun -np $SLURM_NTASKS gmx_mpi make_ndx
mpirun -np $SLURM_NTASKS gmx_mpi grompp
mpirun -np $SLURM_NTASKS gmx_mpi mdrun
GROMACS Program Quick List¶
Below is a quick reference list of the different programs that make up the GROMACS suite.
|gmx||The Single-Node Only Binary|
|gmx_mpi||The main MPI Enabled GROMACS binary|