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 <[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]
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------
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
------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
