Re: [AMBER] restart file position

From: Jason Swails <>
Date: Wed, 29 Oct 2014 13:17:22 -0400

On Wed, Oct 29, 2014 at 11:31 AM, Fabian Glaser <>

> Hi all,
> I noticed that in my amber installation, when using the PBS queue system,
> the -r flag has to be in the last place of the mpirun command:
> mpirun pmemd.MPI -O -i -o eq3.out -p
> ../clec2_system_ETA_ETA_9.prmtop -c eq2.rst -ref
> ../clec2_system_ETA_ETA_9.prmcrd -x -r eq3.rst
> Otherwise the restart file name produced is the default restrt name and
> not as in the case above command eq3.rst

​This doesn't make any sense to me, and I've never seen this happen before.

> ​​
> Any idea why or if I can somehow overcome this problem in a simple way?

​My guess is that there was a typo in the original command somewhere that
caused this problem. If you can't figure out where the typo might be,
provide the (full) contents of the script that displays this strange

​and we may be able to help.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Oct 29 2014 - 10:30:02 PDT
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