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Purpose: Molecular Dynamics
Latest version: 2019.1
License: (tick) Free of use
              GNU LGPL
Website: http://www.gromacs.org/_ext-link

Gromacs is a program for general molecular dynamics, notable for its fast computation of 1-4 interactions.

It can implement regular molecular dynamics simulations using a variety of integrators, Langevin dynamics, energy minimisation, test-particle insertion, etc. It implements a variety of methods to calculate electrostatics and Van der Waals interactions, thermostats and barostats, 2- and 3-dimensional periodic boundary conditions, etc.

SLURM Submit script example

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 external link for more details.

gromacs_example.slm
#!/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.trp \
  -g gromacs_example.log \
  -o gromacs_example.cpt \
  -c gromacs_example.gro \
  -e gromacs_example.edr
 
cp ./{*.log,*.cpt,*.gro,*.edr} ${SLURM_SUBMIT_DIR}

Sbatch options:

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.

  • -J: Name for the job's allocation.
  • -e: Name of the sterr redirection filename.
  • -o: Name of the stdout redirection filename.
  • -p: Name of the partition (queue) where the job will be submited.

  • -n: Number of tasks.

  • -t: Set the job's time limit. If the job don't finish before the time runs out, it will be killed.


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.

  • -s: Input file (.tpr .tpb .tpa).
    • Contains the topology of the system.
  • -g: Output log file.
  • -o: Output trajectory file (.trr .cpt .trj .tng).
    • Contains coordinates, velocities and, optionally, forces.
  • -c: Output structure file (.gro .g96 .pdb .brk .ent .esp).
    • Contains the coordinates and velocities of last step.
  • -e: Output energy file (.edr).
    • Contains energies, temperature, pressure, etc.



Tutorial

You can follow this tutorial about simulation of a protein with Gromacs to get hands-on with the program.



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