<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thank you for all your answers. It reassures me that the problem I encountered wasn't only a secluded case.<div>I can also confirm that the -mol options seems to be the one making the most consumption of the resources - without it memory usage has dropped to 20 gb.</div><div>And it could be connected to dealing with the PBC, as during my simulation lipids cross very often the boundary between system and its images.</div><div><br></div><div>S³awomir</div><div> <div><br></div><div><br><div><div>Wiadomo¶æ napisana przez Matthew Zwier w dniu 2011-07-07, o godz. 16:02:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>I just experienced this myself. The problem appeared to manifest<br>itself when I was using -mol on a molecule that straddled the box<br>wall. Memory usage was extremely high and the resulting MSD plot did<br>not show any linear behavior. Imaging the trajectory with -pbc nojump<br>made g_msd's memory usage drop dramatically and produce a MSD plot<br>more like what I would expect -- a linear region on the 10s of ns<br>scale bookended by nonlinear regions. In this latter case, the<br>results with and without -mol, though not numerically identical, are<br>at least approximately equal. So, it looks like PBC handling may be<br>at fault for one or both of the problems (memory usage and results<br>with/without -mol) here.<br><br>Regardless of whether this is a bug or a natural consequence of trying<br>to do a MSD calculation on broken molecules, the documentation for<br>g_msd implies that g_msd handles periodic boundary conditions<br>implicitly; perhaps the documentation should be updated to emphasize<br>the (in hindsight, completely logical) fact that molecules need to be<br>whole before running g_msd -mol.<br><br>MZ<br>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; 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: 0px; font-size: medium; "><div><div>S³awomir Stachura</div><div>Centre de Biophysique Moléculaire, CNRS<br>Rue Charles Sadron<br>45071 Orléans CEDEX 2<br>France<br><br>E-Mail : <a href="mailto:gerald.kneller@cnrs-orleans.fr">slawomir.stachura@cnrs-orleans.fr</a></div><div><a href="mailto:gerald.kneller@cnrs-orleans.fr"></a>E-Mail : <a href="mailto:stachura.slawomir@gmail.com">stachura.slawomir@gmail.com</a><br>URL : <a href="http://dirac.cnrs-orleans.fr/">http://dirac.cnrs-orleans.fr</a> <br><br>Synchrotron SOLEIL - Division Expériences<br>Saint Aubin - BP 48<br>91192 Gif-sur-Yvette CEDEX<br>France<br><br>Tel : +33 (0)1 69 35 97 51<br><br></div><div><br></div></div><div><br></div></span><br class="Apple-interchange-newline">
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