[gmx-users] g_analyze - negative parameters
gmx3 at hotmail.com
Tue Feb 2 08:54:33 CET 2010
Your data might have intrinsically strange time correlations,
but the chances are high that you have not sampled enough.
I would first also try the g_analyze of Gromacs 4.0, I have improved
some subtleties in the fitting weights there, which can help in certain
But tau1 seems extremely long, or does your input have even longer times?
> From: maximilian.andrews at tu-dortmund.de
> To: gmx-users at gromacs.org
> Date: Mon, 1 Feb 2010 19:49:17 +0100
> Subject: [gmx-users] g_analyze - negative parameters
> Dear Gromacs-Users,
> I've been trying to figure out g_analyze for a while now (having read
> the manual references and papers), but I still haven't found out what
> a negative parameter obtained during fitting means. It's clear that
> when Tau2 is longer than the total simulation time the sampling is
> bad, but I don't know how to interpret a negative parameter and how it
> affects the sampling, as can be seen from the output excerpt obtained
> from the following command (in Gromacs 3.x):
> g_analyze -f data.xvg --ee data_ee.xvg
> a fitted parameter is negative
> invalid fit: e.e. 0.9166 a 0.0376076 tau1 -21618.1 tau2 383059
> Set 1: err.est. 61.1951 a 1 tau1 1.63958e+09 tau2 0
> I'm interested in the average value and the error estimate, but I
> obviously would like to know if my data is good. I guess that since
> Tau2 is set to zero, I only have the short time correlation, and not the
> long time one.
> Thanks in advance for your time!
> Best regards,
> Dortmund University of Technology
> Department of Chemistry
> Physical Chemistry I - Biophysical Chemistry
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