A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
Description
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
Read more on the GROMACS home page.
For a manual consult the the GROMACS home page.
Modules
Version | Installation Path | modulefile | compiler | comment |
---|---|---|---|---|
2018.4 | /sw/chem/gromacs/2018.4/skl/impi | gromacs/2018.4 | intelmpi | |
2018.4 | /sw/chem/gromacs/2018.4/skl/impi-plumed | gromacs/2018.4-plumed | intelmpi | with plumed |
2019.6 | /sw/chem/gromacs/2019.6/skl/impi | gromacs/2019.6 | intelmpi | |
2019.6 | /sw/chem/gromacs/2019.6/skl/impi-plumed | gromacs/2019.6-plumed | intelmpi | with plumed |
Usage
Load the necessary modulefiles. Note that Intel MPI module file should be loaded first
module load impi/2019.5 gromacs/2019.6
This provides access to the binary gmx_mpi wich can be used to run simulations with sub-commands as gmx_mpi mdrun
In order to run simulations MPI runner should be used:
mpirun gmx_mpi mdrun MDRUNARGUMENTS
Job Script Examples
A simple case of a GROMACS job using a total of 640 CPU cores for 12 hours
#!/bin/bash #SBATCH -t 12:00:00 #SBATCH -p standard96 #SBATCH -n 640 export SLURM_CPU_BIND=none module load impi/2019.5 module load gromacs/2019.6 mpirun gmx_mpi mdrun MDRUNARGUMENTS