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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>You don’t need to use –np 4 option to do preprocessing on
version 4.0.4.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Just do preprocessing without it and use it when you start your
simulation like followings:<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>grompp<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>mpirun –np 4 mdrun (if you use MPI for parallel running)<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>kyungchan<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>Halie Shah<br>
<b>Sent:</b> Wednesday, April 22, 2009 4:01 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] np command with GROMACS 4.0.4<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><br>
Hi!<br>
<br>
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:<br>
<br>
<span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>grompp -np 4
-f pr.mdp -c BR6_em.pdb -p BR6.top -o BR6_pr.tpr -n prot.ndx -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 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?<br>
<br>
Thanks so much!<br>
<br>
Halie Shah<br>
University of Houston, TX U.S.<br>
Briggs Lab</span><o:p></o:p></p>
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