[gmx-users] np command with GROMACS 4.0.4

David van der Spoel spoel at xray.bmc.uu.se
Wed Apr 22 22:06:37 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.

Just obey the almighty grompp and don't bother it with trivialities as 
the number of processors. Such futilities have been transferred to the 
able mdrun program.

> 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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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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