[gmx-users] mpirun

Justin Lemkul jalemkul at vt.edu
Mon Nov 9 14:31:52 CET 2015

On 11/9/15 5:23 AM, Said wrote:
> Hi,
> I have a gateway access to uppmax. I could have copied 1aki.pdb to my
> account using box.com since scp does not work.
> when writing mpirun -np 1 pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water
> spce,
> it gives me an error with exit code: 225.

There is not point trying to run pdb2gmx with mpirun; preparation steps should 
usually be done interactively, ideally on a local machine, and the .tpr file 
sent to the cluster to execute mdrun.  Most preparation programs need some kind 
of interactive input, which can be scripted but it is not always obvious what 
needs to be done ahead of time, especially something as complex as pdb2gmx.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list