[gmx-users] using mdrun in the supercomputer

Justin A. Lemkul jalemkul at vt.edu
Thu Dec 31 19:29:32 CET 2009

Asmaa Elsheshiny wrote:
> 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?

It is very rare that mdrun exits without reporting an error message upon 
abnormal termination.  Is the mdrun executable actually MPI-enabled?  Does the 
log file show anything?


> Kind regards,
> Asmaa


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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