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GROMACS is a versatile package to perform molecular dynamics, i.e. to 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 nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. (From

NERSC provides modules for Gromacs.

Use the module avail command to see what versions are available:

nersc$ module avail gromacs


See the example jobs page for additional examples and information about jobs.


#SBATCH --qos=regular
#SBATCH --time=01:00:00
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=64
#SBATCH --cpus-per-task=4
#SBATCH --constraint=cpu

module load gromacs
srun -n 128 mdrun_mpi_sp >& test.log



If after consulting with the above you believe there is an issue with the NERSC module, please file a support ticket.