Halie Shah wrote:

Hi!

I am trying to do my position restrained dynamic simulation on GROMACS 4.0.4, and I want to use 4 nodes on the cpu cluster available at my campus; I typed in the following grompp command:

grompp -np 4 -f pr.mdp -c BR6_em.pdb -p BR6.top -o BR6_pr.tpr -n prot.ndx -maxwarn 10

and it gave me the response that -np is an invalid command.

How do I get grompp to rec. that I want to use 4 processors? Because my job script where I have specified 4 nodes, will not work unless I have np 4 included in my grompp. I did see that it works with GROMACS 3.3.3...but is there a way to do it with 4.0.4?


The option is unnecessary as of version 4.0; the .tpr file produced can be run on any amount of nodes.

-Justin

Thanks so much!

Halie Shah
University of Houston, TX U.S.
Briggs Lab


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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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