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 <[EMAIL PROTECTED]> 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: [EMAIL PROTECTED]
AND
Department of Bioinformatics
Collegium Medicum Jagiellonian University
e-mail: [EMAIL PROTECTED]
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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Institute of Biochemistry
University of Zurich
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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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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