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

Dr. Vitaly Chaban vvchaban at gmail.com
Fri Oct 19 17:31:06 CEST 2012

> 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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