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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, 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.

Available versions of GROMACS in ULHPC

To check available versions of GROMACS at ULHPC type module spider gromacs. The following list shows the available versions of GROMACS in ULHPC.

bio/GROMACS/2016.3-intel-2017a-hybrid
bio/GROMACS/2016.5-intel-2018a-hybrid
bio/GROMACS/2019.2-foss-2019a
bio/GROMACS/2019.2-fosscuda-2019a
bio/GROMACS/2019.2-intel-2019a
bio/GROMACS/2019.2-intelcuda-2019a

Interactive mode

To try GROMACS in the interactive mode, please follow the following steps:

# From your local computer
$ ssh -X iris-cluster

# Reserve the node for interactive computation
$ salloc -p interactive --time=00:30:00 --ntasks 1 -c 4 --x11 # OR si --x11 [...]

# Load the module gromacs and needed environment 
$ module purge
$ module load swenv/default-env/devel # Eventually (only relevant on 2019a software environment) 
$ module load bio/GROMACS/2019.2-intel-2019a

$ gmx_mpi mdrun <all your GMX job specification options in here>

Batch mode

#!/bin/bash -l
#SBATCH -J GROMAC
#SBATCH -N 2
#SBATCH -A <project name>
#SBATCH -M --cluster iris 
#SBATCH --ntasks-per-node=28
#SBATCH --time=00:30:00
#SBATCH -p batch

# Load the module gromacs and needed environment 
module purge
module load swenv/default-env/devel # Eventually (only relevant on 2019a software environment) 
module load bio/GROMACS/2019.2-intel-2019a

srun -n ${SLURM_NTASKS} gmx_mpi mdrun <all your GMX job specification options in here>

Additional information

To know more information about GROMACS tutorial and documentation, please refer to GROMACS documentation.

Tip

If you find some issues with the instructions above, please report it to us using support ticket.


Last update: April 1, 2021