<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>Thanks Berk,<div><br><div>yes, it was an older version. And I did have separate pme nodes when posre was working. So now I'm trying out the new CVS version.</div><div><br></div><div>Andrea</div><div><br></div><div><div><div>On Jul 21, 2008, at 1:53 PM, Berk Hess wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; "><div class="hmmessage" style="font-size: 10pt; font-family: Tahoma; "><div style="text-align: left; ">Hi,<br><br>There was a bug with PME and position restraints in the CVS version,<br>but that has been fixed a month ago. This bug has exactly the behavior<br>you describe, posres should work ok with separate pme nodes (nnodes >= 12),<br>but not without (1 < nnodes < 12).<br><br>So I assume you are not using the most recent CVS version?<br><br>Berk.<br></div><br><hr id="stopSpelling">> Date: Tue, 15 Jul 2008 18:17:10 +0200<br>> From:<span class="Apple-converted-space"> </span><a href="mailto:vaiana@physik.uni-bielefeld.de">vaiana@physik.uni-bielefeld.de</a><br>> To:<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> Subject: [gmx-users] cvs version and position restraints...<br>><span class="Apple-converted-space"> </span><br>> Hi everyone,<br>><span class="Apple-converted-space"> </span><br>> I have a small DNA duplex in a dodecahedron box. Amber forcefield. Spce<span class="Apple-converted-space"> </span><br>> water. I have position restraints defined for the whole duplex in my<span class="Apple-converted-space"> </span><br>> topology. I'm running exactly the same input script on 2, 4 and on 12<span class="Apple-converted-space"> </span><br>> cpus. The one with 12 produces a trajectory in which it is quite clear<span class="Apple-converted-space"> </span><br>> that the restraints are working: the stronger the restraints on a given<span class="Apple-converted-space"> </span><br>> set of atoms, the less these atoms move away from the equilibrium<span class="Apple-converted-space"> </span><br>> position during the simulation. With 4 and 2 cpus, it is af if no<span class="Apple-converted-space"> </span><br>> restraints are used (the whole system tumbles and moves around the box),<span class="Apple-converted-space"> </span><br>> although I do see energy terms for the restraints in the log file...<br>> I'm using the CVS version (downloaded June 4th).<br>> I'm not sure but I think I remember someone having a similar problem on<span class="Apple-converted-space"> </span><br>> version 3.2 but I don't remember how/if it was solved. I couldn't find<span class="Apple-converted-space"> </span><br>> anything on the mailing lists.<br>> Any clue about what's going on?<br>><span class="Apple-converted-space"> </span><br>> Thanks,<br>> Andrea<br>><span class="Apple-converted-space"> </span><br>><span class="Apple-converted-space"> </span><br>> _______________________________________________<br>> gmx-users mailing list<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>><span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<span class="Apple-converted-space"> </span><br>> www interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br><br><hr>Express yourself instantly with MSN Messenger!<span class="Apple-converted-space"> </span><a href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/" target="_new">MSN Messenger</a><span class="Apple-converted-space"> </span>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. Use the<span class="Apple-converted-space"> </span><br>www interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></div></span></blockquote></div><br></div></div></body></html>