GROMACS

Last Update: 25 Nov. 2024

GROMACS is a molecular mechanics and dynamics simulation program developed by a team of members mainly from Sweden and spread across the world. It is available under the LGPL license, and is highly regarded for its rich functionality and high speed.

Available users

Kyushu Univ. users	Academic users	Non-academic users
OK	OK	OK

Module

Module name	Version
gromacs	2024.2
gromacs-cuda	2024.2

Refer to the following page for the usage of modules:
Module usage

Usage

Setup Environment

GROMACS CPU

$ module load intel/2024.1
$ module load impi
$ module load gromacs

GROMACS GPU

$ module load gcc-toolset
$ module load cuda
$ module load ompi-cuda
$ module load gromacs-cuda

Gromacs should be executed as a batch job.

Batch processing script description example (MPI)

#!/bin/bash

#PJM -L rscgrp=a-batch
#PJM -L node=1
#PJM --mpi proc=32
#PJM -L elapse=2:00:00
#PJM -j

module load intel/2024.1
module load impi
module load gromacs

export OMP_NUM_THREADS=2

mpiexec gmx_mpi mdrun -deffnm ion_channel

1 node, 32 processes, 2 threads
Loading an input file ion_channel.tpr.

Batch processing script description example (GPU)

#!/bin/bash

#PJM -L rscgrp=b-batch
#PJM -L node=1
#PJM --mpi proc=4
#PJM -L elapse=2:00:00
#PJM -j

module load gcc-toolset
module load cuda
module load ompi-cuda
module load gromacs-cuda

export OMP_NUM_THREADS=2

mpirun -map-by ppr:4:node gmx_mpi mdrun -deffnm ion_channel

1 node (exclusive use), 4 processes, 2 thread, 4 GPU
Loading an input file ion_channel.tpr.