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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