[gmx-users] np command with GROMACS 4.0.4

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 22 22:05:47 CEST 2009

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.


> 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


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