[gmx-users] Re: np command with GROMACS 4.0.4

Vitaly V. Chaban vvchaban at gmail.com
Wed Apr 22 22:36:51 CEST 2009

If seems in the gmx versions above 4.0 '-np'  is not used. If I am not
mistaken you should just point out the number of nodes in your queueing
system while submitting the job.


> 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?
> Thanks so much!
> Halie Shah
> University of Houston, TX U.S.
> Briggs Lab
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