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<br><br>> Date: Mon, 27 Jul 2009 11:12:16 +0200<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] diffusion, g_msd and trestart<br>> <br>> Enemark Soeren wrote:<br>> > Dear all,<br>> > <br>> > I am trying to calculate diffusion coefficients for a system of (30) <br>> > glycine molecules in a box with (1000) water.<br>> > <br>> > <br>> > <br>> > After running:<br>> > <br>> > g_msd –f md.xtc –s md.tpr –mol –n molindex.ndx<br>> > <br>> > <br>> > <br>> > I get a list of diffusion coefficients – one for each glycine molecule. <br>> > I then calculate the average and the stdev:<br>> > <br>> > <br>> > <br>> > Average=1.004<br>> > <br>> > Stdev=0.7661<br>> > <br>> > <br>> > <br>> > My problem is that the stdev is very great! More than +/- 75% of the <br>> > average value.<br>> > <br>> > Why is that?<br>> <br>> Short simulation most likely. Since these things are big it takes a long <br>> time to equilibrate.<br>> <br><br>Also it depends on what you expect.<br>stdev is not a standard error estimate of the average.<br>It is the spread around the average for all molecules.<br>If all the msd values of the molecules are uncorrelated,<br>which they might or might not be, the error estimate would be stdev/sqrt(30).<br><br>Berk<br><br>> > <br>> > <br>> > <br>> > Also, what is the reason for the trestart=10 default value? Shouldn’t it <br>> > be better to have trestart=1, if my xtc file is saved every 1 ps?<br>> <br>> No, because there is correlation in the system. Ideally you would take <br>> this time to be longer than the correlation time. You could try to find <br>> an estimate of that from the velocity autocorrelation.<br>> <br>> <br>> > <br>> > <br>> > <br>> > Thanks,<br>> > <br>> > Soren Enemark<br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php<br>> <br>> <br>> -- <br>> David van der Spoel, Ph.D., Professor of Biology<br>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>> spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php<br><br /><hr />What can you do with the new Windows Live? <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Find out</a></body>
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