[gmx-users] np command with GROMACS 4.0.4

kyungchan chae ckcumaa at umich.edu
Wed Apr 22 22:06:45 CEST 2009

You don't need to use -np 4 option to do preprocessing on version 4.0.4.

Just do preprocessing without it and use it when you start your simulation
like followings:



mpirun -np 4 mdrun (if you use MPI for parallel running)




From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Halie Shah
Sent: Wednesday, April 22, 2009 4:01 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] np command with GROMACS 4.0.4



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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