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.

Usage

GROMACS software can be loaded using one of the following module load commands:

$ module load GROMACS/2021-foss-2020b
$ module load GROMACS/2019.3-foss-2019b

The GROMACS executable is gmx or gmx_mpi if using an OpenMPI module. Typing gmx help commands will display a list of commands for gmx and their function.

Interactive usage

For interactive usage during testing etc… we recommend using a non-GPU, non-MPI module e.g. GROMACS/2021-foss-2020b. You can load this and run gmx commands as follows:

$ module load GROMACS/2021-foss-2020b
$ gmx help commands

Batch jobs

Users are encouraged to write their own batch submission scripts. The following are example batch submission scripts, my_job.sh, to run gmx or gmx_mpi which are submitted to the queue by typing sbatch my_job.sh.

Warning

To get optimal parallelisation of GROMACS sub-commands, users should consult the GROMACS documentation to determine which of the commands have parallelisation enabled. For example, mdrun is parallelisable where grompp and many others are not.

Please also ensure you consult the right version of the documentation as more modern versions of GROMACS are likely to have numerous differences.

GROMACS can run using in smp parallel environment, in addition to being able to use GPU acceleration. Examples of these types of batch submission can be seen below.

Using GMX

The following is an example batch submission script, my_job.sh, to run the gromacs executable gmx with input files grompp.mdp, conf.gro and topol.top. The script requests 5 GB of real memory.

The GROMACS input line beginning with gmx grompp is to make a run input file; gmx mdrun is to perform a simulation, do a normal mode analysis or an energy minimization.

The export command sets the correct number of GROMACS threads based on the requested number of cores from the scheduler (important if requesting more than a single core).

#!/bin/bash
# Request 5 gigabytes of real memory (mem)
#SBATCH --mem=5G
#SBATCH --time=00:30:00
# Email notifications to me@somedomain.com
#SBATCH --mail-user=me@somedomain.com
# Email notifications if the job fails
#SBATCH --mail-type=FAIL

module load GROMACS/2021-foss-2020b

# Set the OPENMP_NUM_THREADS environment variable to the number of available cores.
# The line ensures that OpenMP uses all of the CPUs allocated to the task
# for parallel processing. This can improve the performance of parallelised
# code by fully utilising the available resources.
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

gmx grompp -f grompp.mdp -c conf.gro -p topol.top -o topol.tpr
gmx mdrun -s topol.tpr

Using GMX_MPI

This script requests four CPU cores and a runtime of 30 minutes. The GROMACS input line beginning with gmx_mpi grompp is to make a run input file; srun -np $NSLOTS gmx_mpi mdrun is to perform a simulation, to do a normal mode analysis or an energy minimization with the correct number of MPI threads.

Note

Note gmx_mpi is used when using OpenMPI functionality and should not be used on interactive sessions.

#!/bin/bash
#SBATCH --mem=5G
#SBATCH --time=00:30:00
#SBATCH --cpus-per-task=4
# Email notifications to me@somedomain.com
#SBATCH --mail-user=me@somedomain.com
# Email notifications if the job fails
#SBATCH --mail-type=FAIL

module load GROMACS/2021-foss-2020b

gmx_mpi grompp -f grompp.mdp -c conf.gro -p topol.top -o topol.tpr
srun -np $SLURM_NTASKS gmx_mpi mdrun -s topol.tpr

Using GPUs

Currently none of the gromacs installations have the CUDA modules. If you need access to them please contact research-it@sheffield.ac.uk

Installation notes

GROMACS was installed using Easybuild 4.7.0, build details can be found in $EBROOTGROMACS/easybuild with the module loaded. GROMACS should just be installed using a batch session otherwise the installation will crash when it comes to build gmx_mpi.

Testing was done using the example on Lysozyme in Water