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.<br><br>Vitaly<br><br><div class="gmail_quote">
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I am trying to do my position restrained dynamic simulation on GROMACS<br>
4.0.4, and I want to use 4 nodes on the cpu cluster available at my campus;<br>
I typed in the following grompp command:<br>
<br>
grompp -np 4 -f pr.mdp -c BR6_em.pdb -p BR6.top -o BR6_pr.tpr -n prot.ndx<br>
-maxwarn 10<br>
<br>
and it gave me the response that -np is an invalid command.<br>
<br>
How do I get grompp to rec. that I want to use 4 processors? Because my job<br>
script where I have specified 4 nodes, will not work unless I have np 4<br>
included in my grompp. I did see that it works with GROMACS 3.3.3...but is<br>
there a way to do it with 4.0.4?<br>
<br>
Thanks so much!<br>
<br>
Halie Shah<br>
University of Houston, TX U.S.<br>
Briggs Lab<br>
<br>
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