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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.
The following file is a Gromacs template job submission script that can used as a starting point for creating your own scripts:
#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 on a sub-directory of your
Submit the job using the following command: