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Information

Purpose: Molecular Dynamics
Latest version: 2018.1
License: GNU LGPL
Website: http://www.gromacs.org/

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.

 

 

Benchmark

Gromacs 5.1.2 benchmark at collserola:

Actual speed-up (green) and ideal speed-up (blue) vs. number of cores for the NPT simulation of a protein with Amber force field, SPC water, PME electrostatics, no PME-dedicated node.

Note that, in runs with a large number of CPUs, performance can improve greatly by finding a correct balance between PME and particle threads in a problem-specific fashion. Here we show default behaviour, without custom optimisations.

 

 

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 gromacs_example
#SBATCH -e gromacs_example.err
#SBATCH -o gromacs_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 < gromacs_example .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.

 

 

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