[gmx-users] topology file

[Justin Lemkul]

On 3/19/14, 2:22 PM, Michelle Aranha wrote:
> I create a parallel job file with the following content
> #$ -N prep66
> #$ -pe openmpi* 12
> #$ -cwd
> #$ -q medium*
>
> mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/editconf_mpi -f 66.pdb -o
> cnt.gro -bt cubic -box 5 5 5 -c
> mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/g_x2top_mpi -f cnt.gro -o
> cnt.top -ff opls -name CNT
> mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/genbox_mpi -cp cnt.gro -cs
> spc216.gro -p cnt.top -o cntsol.gro
> mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/genrestr_mpi -f cntsol.gro
>
> During the process of running it creates several temp.top files which have
> the correct output, however the final topology file I get has zero output.
> I would like to know if I am doing anything wrong.
>

The only Gromacs executable that is parallelized is mdrun.  Run the others in 
serial.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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