[gmx-users] np command with GROMACS 4.0.4

Halie Shah haliepshah at gmail.com
Wed Apr 22 22:01:00 CEST 2009


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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