GROMACS

• General Information
• Usage on Vilje
  • Sample GROMACS Job Script
• Further Information

General Information

Home page	Version	Module dependencies
		Compiler	MPT
www.gromacs.org	2016.1	intelcomp/17.0.0	mpt/2.14

GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but GROMACS is also used for research on non-biological systems, e.g. polymers.

Usage on Vilje

Load the intelcomp, mpt and gromacs modules to use GROMACS on Vilje:

$ module load intelcomp/17.0.0 mpt/2.14 gromacs/2016.1

Sample GROMACS Job Script

#!/bin/bash
###################################################
#
#  GROMACS job
#
###################################################
#
#PBS -N test
#PBS -A nn1234k
#PBS -l select=2:ncpus=32:mpiprocs=16
#PBS -l walltime=24:00:00
#
 
module load intelcomp/17.0.0
module load mpt/2.14
module load gromacs/2016.1
 
case=$PBS_JOBNAME
 
cd $PBS_O_WORKDIR
 
# Create (if necessary) the working directory
w=/work/$PBS_O_LOGNAME/gromacs/$case
if [ ! -d $w ]; then mkdir -p $w; fi
 
# Copy inputfiles and move to working directory
cp $case.tpr $w
cd $w

mpiexec_mpt mdrun $case.tpr

Further Information

• GROMACS Documentation