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Gromacs

GROMACS is a package to perform molecular dynamics simulations, i.e., compute the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have many complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations), many groups are also using it for research on non-biological systems.

How to use

  1. Create the input files:

    water.gro
    Water molecule
3
    1WAT     OW    1   0.000   0.000   0.000
    1WAT    HW1    2   0.000   0.100   0.000
    1WAT    HW2    3   0.100   0.000   0.000
   0.200   0.200   0.200
EOL
    water.mdp
    ; Run parameters
integrator               = md
dt                       = 0.002
nsteps                   = 500000
; Output parameters
nstxout                  = 500
nstvout                  = 500
nstenergy                = 500
nstlog                   = 500
; Bond parameters
continuation             = no
constraint_algorithm     = lincs
lincs_iter               = 1
lincs_order              = 4

    water.top
    ; Include forcefield parameters
#include "oplsaa.ff/forcefield.itp"
[ system ]
; Name
Water molecule
[ molecules ]
; Compound        #mols
SOL               1
    For more information about these files and what the options mean, we highly recommened the GROMACS tutorials.

  2. Create your submission script and submit your job to the scheduler

    gromacs-slurm.sh
    #!/bin/bash
#SBATCH --job-name=gromacs_test
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=48
#SBATCH --time=01:00:00
#SBATCH --partition=bsudfq


module load borah-applications gromacs/2022.3/openmpi/4.1.3/gcc/12.1.0  

gmx_mpi pdb2gmx -f water.pdb -o water_processed.gro -water spce
gmx_mpi grompp -f water.mdp -c water_processed.gro -p water.top -o water.tpr

mpirun gmx_mpi mdrun -v -deffnm water

    Submit the job 

    sbatch gromacs-slurm.sh

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