Dear gromacs users,
I tried to make MD simulation using mdrun in the super computer by using the
following script:
#!/bin/sh
#$ -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,
Asmaa
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