[gmx-users] Re: Changing md command line in a script!

Arman Mahboubi Soufiani armansoufiani at gmail.com
Fri Oct 19 17:35:11 CEST 2012

Dear Vitaly,

I appreciate your informative response.

Dear Justin,

Thank you for your kind helps.

On Fri, Oct 19, 2012 at 5:31 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:

> > Dear all,
> >
> > A simple question.
> > I want to change the md command line in a script. I want to prevent my
> > script to lead the simulation on parallel nodes. By this I mean I want to
> > run it on one CPU. I do not know where I should embed the flag -nt=1 in
> that
> > command lien.
> > I wonder the following is the md command? If yes, how it will become when
> > adding -nt=1 to it?
> You need to remove the MPI program at the very beginning of the line,
> if you have any.
> You may also specify "-nt 1" as the mdrun option. My new workstation,
> for instance, tries to simulate with "-nt 12", even if I do not ask
> for this.
> All other utilities will be executed using 1 processor, regardless of
> what you request on the command line.
> Dr. Vitaly V. Chaban
> MEMPHYS - Center for Biomembrane Physics
> Department of Physics, Chemistry and Pharmacy
> University of Southern Denmark
> Campusvej 55, 5230 Odense M, Denmark
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