<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Amin,<div><br></div><div>the -np flag is not necessary any more for grompp in Gromacs 4.0.</div><div>For mdrun, just use something like</div><div>mpirun -np 4 mdrun -s topol.tpr</div><div><br></div><div>Carsten</div><div><br></div><div><br><div><div>On Jun 21, 2010, at 2:00 PM, Amin Arabbagheri wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><table cellspacing="0" cellpadding="0" border="0"><tbody><tr><td valign="top" style="font: inherit;">Hi all,<br><br>I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic package manager.<br>I want to run a simulation in parallel on a multi processor, single PC, but to compile via grompp, it doesn't accept -np flag, and also , using -np in mdrun, it still runs as a single job.<br>Thanks a lot for any instruction.<br><br>Bests,<br>Amin<br><br></td></tr></tbody></table><br>
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<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br class="Apple-interchange-newline">--</div><div>Dr. Carsten Kutzner</div><div>Max Planck Institute for Biophysical Chemistry</div><div>Theoretical and Computational Biophysics</div><div>Am Fassberg 11, 37077 Goettingen, Germany</div><div>Tel. +49-551-2012313, Fax: +49-551-2012302</div><div><a href="http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne">http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne</a></div><div><br></div></div><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></span>
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