[gmx-users] quasiharmonic eigenvalue units / Schlitter entropy

[David van der Spoel]

Ran Friedman, Biochemisches Inst. wrote:
> 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-?).
Yes indeed. Please compare the results with your script.

> 
> 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
> ------------------------------------------------------
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se