Benchmark
SLURM Submit script example
For more information use 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.
adf_example.slm
#!/bin/bash #SBATCH -J gaussian_example #SBATCH -e gaussian_example.err #SBATCH -o gaussian_example.out #SBATCH -p std #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=1 #SBATCH --mem=4G module load apps/gromacs/2018.1 INPUT_DIR=${PWD} OUTPUT_DIR=${PWD} cd $TMPDIR cp -r $INPUT_DIR $TMPDIR mpirun -np 24 -tmintel gmx_mpi mdrun -s < default .trp file > cp ./* $OUTPUT_DIR
Tutorial
You can follow this tutorial about simulation of a protein with Gromacs to get hands-on with the program.