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More information about the submit script can be found using the Job Script Generator.
For optimal performance, before a long production run, you are advised to experiment with different thread allocations to PME and DD tasks, using mdrun options. Please refer to the Gromacs documentation for more details. |
#!/bin/bash #SBATCH -J gromacs_example #SBATCH -e gromacs_example.err #SBATCH -o gromacs_example.out #SBATCH -p std #SBATCH --ntasks=24 module load apps/gromacs/2019.1 ## # Modify the input and output files! cp -r ${SLURM_SUBMIT_DIR}/*.trp ${SCRATCH} cd ${SCRATCH} srun gmx_mpi mdrun \ -s gromacs_example.tpr \ -g gromacs_example.log \ -o gromacs_example.trr \ -c gromacs_example.gro \ -e gromacs_example.edr cp ./{*.log,*.cpt,*.gro,*.edr} ${SLURM_SUBMIT_DIR} |
The options shown in the example are detailed below. For more information and a more comprehensive list of available options, see the sbatch command page.
-n: Number of tasks.
Software execution information:
The mdrun program is the main program of Gromacs. It can perform Molecular Dynamics, Stochastic Dynamics, Energy Minimisation, test particle insertion or (re)calculation of energies.
You can follow this tutorial about a protein's simulation using Gromacs to get hands-on with the program.