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howto:gromacs

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Gromacs

Initial Setup

In order to use Gromacs append the following lines to your .profile file:

export MODULEPATH=/opt/gridware/applications/gromacs/modules:$MODULEPATH
module add gromacs/4.6.1 mpich2/1.5

To complete the setup log out of the cluster and back in again (or just source your .profile file) to update your environment variables.

Example Job Submission Script

The following file is a Gromacs template job submission script that can used as a starting point for creating your own scripts:

gromacs.job
#This job tests GROMACS, it requires the input file min.steep0.tpr to be in the working directory.
 
#MSUB -l nodes=2:ppn=12
#MSUB -l feature=dell
#MSUB -l walltime=24:00:00
#MSUB -j oe
#MSUB -o out.log
#MSUB -d /export/home/username/scratch5/gromacs
#MSUB -V
 
NP=`cat $PBS_NODEFILE | wc -l`
BIN=mdrun_mpi
ARGS="-s min.steep0.tpr -deffnm min.steep0 -npme 4"
 
mpirun -np $NP -machinefile $PBS_NODEFILE $BIN $ARGS

This job submission script requires that the file min.steep0.tpr be in the working directory specified above.

NOTE: Please ensure that all file I/O associated with your job only occurs in a sub-directory of the scratch5 partition.

Job Submission

Submit the job using the following command:

msub gromacs.job

Example Expected Output

/var/www/wiki/data/attic/howto/gromacs.1385130909.txt.gz · Last modified: 2013/11/22 16:35 by swyngaard