[gmx-users] RE: quasi-harmonic entropy calculation

Ran Friedman ran.friedman at lnu.se
Thu Mar 22 19:58:54 CET 2012

IIRC I tested g_anaeig when David wrote it and the results were the same as calc_entropies.pl, so it sounds strange. Are you sure you use the same input in both cases? Did you use the eigenvectors that correspond to the same eigenvalues? Also, how may eigenvalues are close to zero?

Message: 4
Date: Thu, 22 Mar 2012 10:27:36 -0400
From: wmiranda at estudiantes.fbio.uh.cu
Subject: [gmx-users] Re: quasi-harmonic entropy calculation
To: gmx-users at gromacs.org
Message-ID: <5e667c140e0c268c9e87681be3535b89.squirrel at est.fbio.uh.cu>
Content-Type: text/plain;charset=iso-8859-1

My name is Williams. I am a Biochemistry student. I have done QH entropy
calculation using g_anaeig, but I found an old perl script at GROMACS web
site to do the same. The problem is that when I calculate entropy for the
loops of my protein the results are the same using g_anaeig or the old
perl script, but when I compare the entropy calculated through both
methods for my entire protein the results diverges in one order of
magnitud and I give to the script the same eigenvalues obtained by g_covar
(g_anaeig uses the eigenvectors). Please, help me.

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