Gromacs

GROMACS

GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported.

Slurm Script

#!/bin/bash
#SBATCH -J my_sim_job
#SBATCH -o my_sim_job.o%j.out
#SBATCH -e my_sim_job.o%j.err

#SBATCH -p CUIQue # Queue name
#SBATCH -t 04:00:00
#SBATCH -N 8 # Total number of nodes requested
#SBATCH -n 128 # Total number of mpi tasks requested

module load gromacs/2021.3

##benchmark set (82k atoms, protein in membrane surrounded by water , 2fs time step)

mpirun gmx_mpi mdrun -s benchMEM.tpr -deffnm gmx_md

Submit the job to the scheduler as

sbatch YourGromacscript.slurm

For managing your “job” , refer to this guide.

For more on GROMACS, refer to their official documentation

https://manual.gromacs.org/documentation/