[gmx-users] using mdrun in the supercomputer

Asmaa Elsheshiny pyaaea at leeds.ac.uk
Thu Dec 31 19:10:38 CET 2009

Dear gromacs users,
I tried to make MD simulation using mdrun in the super computer by using the following script:
#$  -cwd  –V
#$  -l h_rt=1:00:00
#$  -pe mx* 4
export  DO_PARALLEL=”/usr/local/sge6.0/mpi/myrinet/sge_mpirun”
export  gromacs=/apps/gromacs/64/3.3.1-ffamber20080701/bin
$ DO_PARALLEL $gromacs/mdrun   “ -s md.tpr  \
             -o md.trr  -x md.xtc  –c md.gro  –e  ener.edr”
This script appears to work fine, but i stopped suddenly after a short period giving missing output. That is why the structure file .gro is missing. I have tested it locally before submitting it as a job in the supercomputer; I found that it works fine. So, what is the problem with this script?
Kind regards,

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