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Hi,<br><br>Your data might have intrinsically strange time correlations,<br>but the chances are high that you have not sampled enough.<br>I would first also try the g_analyze of Gromacs 4.0, I have improved<br>some subtleties in the fitting weights there, which can help in certain<br>unstable cases.<br>But tau1 seems extremely long, or does your input have even longer times?<br><br>Berk<br><br>> From: maximilian.andrews@tu-dortmund.de<br>> To: gmx-users@gromacs.org<br>> Date: Mon, 1 Feb 2010 19:49:17 +0100<br>> Subject: [gmx-users] g_analyze - negative parameters<br>> <br>> Dear Gromacs-Users,<br>> <br>> I've been trying to figure out g_analyze for a while now (having read<br>> the manual references and papers), but I still haven't found out what<br>> a negative parameter obtained during fitting means. It's clear that<br>> when Tau2 is longer than the total simulation time the sampling is<br>> bad, but I don't know how to interpret a negative parameter and how it<br>> affects the sampling, as can be seen from the output excerpt obtained<br>> from the following command (in Gromacs 3.x):<br>> <br>> g_analyze -f data.xvg --ee data_ee.xvg<br>> <br>> a fitted parameter is negative<br>> invalid fit: e.e. 0.9166 a 0.0376076 tau1 -21618.1 tau2 383059<br>> Set 1: err.est. 61.1951 a 1 tau1 1.63958e+09 tau2 0<br>> <br>> I'm interested in the average value and the error estimate, but I<br>> obviously would like to know if my data is good. I guess that since<br>> Tau2 is set to zero, I only have the short time correlation, and not the<br>> long time one.<br>> <br>> Thanks in advance for your time!<br>> <br>> Best regards,<br>> <br>> Maximilian<br>> -- <br>> Dortmund University of Technology<br>> Department of Chemistry<br>> Physical Chemistry I - Biophysical Chemistry<br>> Otto-Hahn-Str. 6<br>> D-44227 Dortmund<br>> Germany<br>> <br>> Office: C1-06 room 176<br>> Phone: +49 231 755 3916<br>> Fax: +49 231 755 3901<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 /><hr />New Windows 7: Simplify what you do everyday. <a href='http://windows.microsoft.com/shop' target='_new'>Find the right PC for you.</a></body>
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