Difference (from prior major revision)
< * Run it : <b>qsub SGE.sh</b> followed by several *qstat* commands to confirm that the job had started.
> * Run it : <b>qsub SGE.sh</b> followed by several *qstat* commands to confirm that the job started.
> * The Gromacs manual is available /via/ the cluster's homepage (documents -> computational biology -> molecular dynamics).
- Create a clean directory in /work/tmp and extract the files :
- cd /work/tmp
- mkdir gtest
- cd gtest/
- mv ~/gromacs_lysozyme_benchmark_files.tar.gz ./ (assuming the browser saved the file in your home directory).
- gunzip gromacs_lysozyme_benchmark_files.tar.gz
- tar xvf gromacs_lysozyme_benchmark_files.tar
- rm gromacs_lysozyme_benchmark_files.tar
- Have a look at the system you will be simulating : vmd conf.gro
- Preparation step (assuming you will run it on two processors) :
/usr/local/gromacs/i686-pc-linux-gnu/bin/grompp -f pme.mdp -c conf.gro -p topol.top -po mdout.mdp -shuffle -sort -np 2
- Prepare a submission script for SGE, say SGE.sh :
- Run it : qsub SGE.sh followed by several qstat commands to confirm that the job started.
- The Gromacs manual is available via the cluster's homepage (documents → computational biology → molecular dynamics).