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.
Vitaly > 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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