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.
This is a GPU enabled build, containing both MPI and threadMPI binaries.
Available Modules¶
module load GROMACS/2021.6-gimkl-2020a-cuda-11.6.2-hybrid-PLUMED-2.8.0GROMACS (the GROningen MAchine for Chemical Simulations) 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 is available to anyone at no cost under the terms of the GNU Lesser General Public Licence. Gromacs is a joint effort, with contributions from developers around the world: users agree to acknowledge use of GROMACS in any reports or publications of results obtained with the Software.
Job submission¶
GROMACS performance depends on several factors, such as usage (or lack thereof) of GPUs, the number of MPI tasks and OpenMP threads, the load balancing algorithm, the ratio between the number of Particle-Particle (PP) ranks and Particle-Mesh-Ewald (PME) ranks, the type of simulation being performed, force field used and of course the simulated system. For a complete set of GROMACS options, please refer to GROMACS documentation.
Within each GRMACS environment module we have two versions of GROMACS,
one built with with "thread-MPI", which is really just
multithreading, and one with real MPI which can run across multiple nodes in
a distributed job, ie: with --ntasks > 1.
In GROMACS/2025.2-foss-2023a-cuda-12.5.0-hybrid and more
recent environment modules the two programs are named gmx and gmx-mpi.
In our older GROMACS environment modules gmx was renamed to gmx-serial.
Unless your problem is so large
that it does not fit on one whole compute node you are probably best
off not using gmx-mpi. The GROMACS documentation says on this:
The thread-MPI library implements a subset of the MPI 1.1 specification, based on the system threading support. … Acting as a drop-in replacement for MPI, thread-MPI enables compiling and running mdrun on a single machine (i.e. not across a network) without MPI. Additionally, it not only provides a convenient way to use computers with multicore CPU(s), but thread-MPI does in some cases make mdrun run slightly faster than with MPI.
Thread-MPI is compatible with most mdrun features and parallelization schemes, including OpenMP, GPUs; it is not compatible with MPI and multi-simulation runs.
GPU support¶
GROMACS is built with CUDA support, but that is optional to use - it will run without a GPU.
MPI¶
If you do elect to use gmx-mpi, note that hybrid parallelisation (ie with --cpus-per-task > 1) can be
more efficient than MPI-only parallelisation. With hybrid parallelisation, it is important to run
mdrun_mpi with the -ntomp <number> option, where <number> should
be the number of CPUs per task. You can make sure the value is correct
by using -ntomp ${SLURM_CPUS_PER_TASK}.
If you use a GPU together with MPI, you may need to set CRAY_CUDA_MPS=1 to enable multiple tasks on one node to access the same GPU device at the same time.
Checkpointing and restarting¶
The -cpt 30 option instructs Gromacs to
write a full checkpoint file every 30 minutes. You can restart from a
checkpoint file using the -cpi flag, thus: -cpi state.cpt.