GROMACS is a software package for molecular dynamics simulations, and OCTOPUS allows the use of GROMACS 2025.2 by batch request. Anyone who has applied to use OCTOPUS is eligible to use it.
 

Basic use

GROMACS execution is only allowed to process by batch request. Connect to the front-end node, create the input file and job script necessary for the calculation, and then submit the job. Examples of job scripts and job execution methods for using GROMACS are described below.
 
* For the manual about GROMACS, please refer to official HP.
 

Writing a Job Script(for General Purpose CPU nodes)

The following example is an example job script when GROMACS is run on 512 parallel (using 2 nodes, 256 parallel per node). Although there is no particular specification for the file name, we named "gromacs.sh" in this section.

gromacs.sh

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#!/bin/bash #PBS -q OCT #PBS -l cpunum_job=256 #PBS --group=[group name] #PBS -b 2 #PBS -T intmpi #PBS -l elapstim_req=01:00:00 #PBS -v OMP_NUM_THREADS=256 module load BaseApp module load gromacs/2025.2 cd $PBS_O_WORKDIR mpirun ${NQSV_MPIOPTS} -np 2 gmx_mpi_d mdrun -s (Input file)


For other lines of the job script, see here.
 

How to execute

You can submit your job script with "qsub" command.

% qsub gromacs.sh

If the execution is successful, the calculation result will be output to the result file.