[gmx-users] g_analyze - negative parameters

Maximilian Andrews maximilian.andrews at tu-dortmund.de
Mon Feb 1 19:49:17 CET 2010

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
Otto-Hahn-Str. 6
D-44227 Dortmund

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