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

David van der Spoel spoel at xray.bmc.uu.se
Thu Mar 22 19:48:01 CET 2012

Op 22 mar 2012 om 15:27 heeft wmiranda at estudiantes.fbio.uh.cu het volgende geschreven:

> 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.
> Thanks

Is there readon to assume g_anaeig is incorrect? There is numerical problem with this calculation due to the large range of numbers and therefore the g_anaeig program uses ligarithms. Please compare the source code in case of doubt.
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