[gmx-users] quasiharmonic eigenvalue units / Schlitter entropy

[Ran Friedman, Biochemisches Inst.]

Dear Marcin,

You can contact me off list for a script that calculates the QH entropies 
from the output of g_covar. Also, IIRC there should be a version of g_covar 
that already does it somewhere (CVS-?).

Ran.

On Wed, 31 Oct 2007 17:40:45 +0000
  Marcin Krol <mykrol at cyf-kr.edu.pl> wrote:
> Dear All,
> 
> Sorry for the repeated question, but I'm a bit lost when I want to get 
>frequencies of modes from quasiharmonic analysis done with g_covar. From 
>what I understood in QH
> omega = sqrt(kT/lambda), where omega is the radial frequency, k - 
>Boltzmann const, T-temp, and lambda is the eigenvalue. In order to get the 
>units right lambda needs to be in length^2*mass units. Is it nm^2*amu?
> I need the frequencies to calculate entropy estimate from QH analysis. 
>However, another way of getting the entropy estimate would be to get it 
>from Schlitter formula. Then, I wouldn't need to diagonalize the covariance 
>matrix. Is there a way to request the calculation of Schlitter entropy 
>after the covariance matrix is calculated, but before g_covar starts 
>diagonalization?
> 
> Thanks in advance
> marcin
> 
> -- 
> Dr Marcin Krol
> Biomolecular Modelling Laboratory
> Cancer Research UK
> e-mail: marcin.krol at cancer.org.uk
> AND
> Department of Bioinformatics
> Collegium Medicum Jagiellonian University
> e-mail: mykrol at cyf-kr.edu.pl
> 
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------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Institute of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6354493
Skype: ran.friedman
------------------------------------------------------