Contents

GROMACS

Overview

GROMACS is a package for computing molecular dynamics, simulating Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is designed for biochemical molecules with complicated bonded interactions (e.g. proteins, lipids, nucleic acids) but can also be used for non-biological systems (e.g. polymers).

Versions 2018.4 and 2020.1 (single and double precision, multi-core and MPI parallel) are installed.

Please do not add the -v flag to your mdrun command.
It will write to a log file every second for the duration of your job and can lead to severe overloading of the file servers.

Significant Change in this Version

Within Gromacs 2018 and 2020, the different gromacs commands (e.g., mdrun, grompp, g_hbond) should now be run using the command:

gmx command

where command is the name of the command you wish to run (without any g_ prefix), for example:

gmx mdrun

The gmx command changes its name to reflect the gromacs flavour being used but the command does not change. For example, if using the mdrun command:

# New 20XY method              # Previous 5.0.4 method (not available on CSF4)
# ===============              # =====================
gmx   mdrun                    mdrun
gmx_d mdrun                    mdrun_d
mpirun gmx_mpi   mdrun         mpirun -n $NSLOTS mdrun_mpi
mpirun gmx_mpi_d mdrun         mpirun -n $NSLOTS mdrun_mpi_d

The complete list of command names can be found by running the following on the login node:

gmx help commands

# The following commands are available:
anadock			gangle			rdf
anaeig			genconf			rms
analyze			genion			rmsdist
angle			genrestr		rmsf
awh			grompp			rotacf
bar			gyrate			rotmat
bundle			h2order			saltbr
check			hbond			sans
chi			helix			sasa
cluster			helixorient		saxs
clustsize		help			select
confrms			hydorder		sham
convert-tpr		insert-molecules	sigeps
covar			lie			solvate
current			make_edi		sorient
density			make_ndx		spatial
densmap			mdmat			spol
densorder		mdrun			tcaf
dielectric		mindist			traj
dipoles			mk_angndx		trajectory
disre			morph			trjcat
distance		msd			trjconv
do_dssp			nmeig			trjorder
dos			nmens			tune_pme
dump			nmtraj			vanhove
dyecoupl		order			velacc
dyndom			pairdist		view
editconf		pdb2gmx			wham
eneconv			pme_error		wheel
enemat			polystat		x2top
energy			potential		xpm2ps
filter			principal
freevolume		rama

Notice that the command names do NOT start with g_ and do NOT reference the flavour being run (e.g., _mpi_d). Only the main gmx command changes its name to reflect the flavour (see below for list of modulefiles for the full list of flavours available).

To obtain more help about a particular command run:

gmx help command

For example

gmx help mdrun

Available Flavours

For versions 2018.4 and 2020.1 we have compiled multiple versions of Gromacs, for CPU jobs only (there are no GPUs in CSF4). You can use single or double precision executables for parallel multi-core (threads) or larger multi-node (MPI) jobs.

Restrictions on use

GROMACS is free software, available under the GNU General Public License.

Set up procedure

You must load one of the following modulefiles:

module load gromacs/2020.1-iomkl-2020.02-python-3.8.2
module load gromacs/2018.4-iomkl-2020.02

The following executables are available for use in your jobscripts:

gmx          # Single precision multicore (single compute node job)
gmx_d        # Double precision multicore (single compute node job)

gmx_mpi      # Single precision MPI (multi-node job)
gmx_mpi_d    # Double precision MPI (multi-node job)

Remember you will need to add the command to be run by gromacs to the gmx command-line in your jobscript. For example:

# Double-precision multicore (single compute node)
gmx_d mdrun args...

Running the application

Please do not run GROMACS on the login node.

Important notes regarding running jobs in batch

We now recommend that the module file is loaded as part of your batch script.

It is not necessary to tell mpirun how many cores to use if using the MPI executables. This is because SLURM knows this automatically.

# Multi-core (single-node) or large Multi-node MPI job. SLURM knows how many cores to use.
mpirun gmx_mpi mdrun     # New method (v5.1.4 and later)
mpirun gmx_mpi_d mdrun   # New method (v5.1.4 and later)

However, if using the multicore (single compute node) executables, you must inform GROMACS how many cores to use with the $SLURM_NTASKS variable:

# Single-node multi-threaded job
export OMP_NUM_THREADS=$SLURM_NTASKS      # Inform GROMACS how many cores to use
gmx mdrun                                 # New method (v5.1.4 and later)
gmx_d mdrun                               # New method (v5.1.4 and later)

The examples below can be used for single precision or double precision GROMACS. Simply run mdrun (single precision) or mdrun_d (double precision).

Please do not add the -v flag to your mdrun command.
It will write to a log file every second for the duration of your job and can lead to severe overloading of the file servers.

Multi-threaded single-precision, 2 to 40 cores

Note that GROMACS 2020.1 (unlike v4.5.4) does not support the -nt flag to set the number of threads when using the multithreaded OpenMP (non-MPI) version. Instead set the OMP_NUM_THREADS environment variable as shown below.

An example batch submission script to run the single-precision mdrun executable with 16 threads:

#!/bin/bash --login
#SBATCH -p multicore     # (--partition=multicore) 
#SBATCH -n 16            # Can specify 2 to 40 cores in the multicore partition
                           
module load gromacs/2020.1-iomkl-2020.02-python-3.8.2
export OMP_NUM_THREADS=$SLURM_NTASKS
gmx mdrun