<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On Feb 11, 2010, at 7:40 PM, Rebeca García Fandiño 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: medium; 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; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; "><font><font size="2" style="font-size: 10pt; ">Hi,<br>I am doing PMF calculations using Gromacs 3.3.3, and I have found very different results using 2 different machines. Attached you can see that the graphics are really different for both cases (about 10 KJ/mol!!). The version of Gromacs (3.3.3) and number of processors used (2) is the same for both calculations. The .tpr files and all the starting files are identical for both calculations. The only thing that changes is the machine where they were carried out.<span class="Apple-converted-space"> </span><br>I have checked the energy files for both cases, and they are different, but taking into account the stochastic effect, I suppose it is normal. There are slight differences in the energies in the step 0 for some of the windows (but in the 5th decimal number, so they should not be important, I suppose). </font></font></div></span></blockquote>Well this might be a problem but the 5th decimal is pretty far.<br><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; 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; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; "><font><font size="2" style="font-size: 10pt; ">Any idea of the cause of the problem? Has anyone experienced similar problems? A</font></font><font><font size="2" style="font-size: 10pt; ">ny suggestion will be much appreciated</font></font>.<br><font><font size="2" style="font-size: 10pt; ">Thanks a lot for your help, in advance.<br></font></font></div></span></blockquote>the only thing you have left is that you have not sampled enought ... so</div><div>you have not reached convergence.</div><div>Did you try to repeat the calculation on the ame machine changing the </div><div>initial velocities ?</div><div><br></div><div><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; 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; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; "><font><font size="2" style="font-size: 10pt; ">Cheers,<br><br>Rebeca Garcia<span class="Apple-converted-space"> </span><br><br></font></font><br><hr>Elige un juego de Messenger. Reta a un amigo.<span class="Apple-converted-space"> </span><a href="http://www.messengergamesclub.com/spain/" target="_new">¡Pruébalo ya!</a><span class="Apple-converted-space"> </span><span><comparation_neuron_ngs.pdf></span>--<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://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.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? 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