[gmx-users] quasiharmonic eigenvalue units / Schlitter entropy
mykrol at cyf-kr.edu.pl
Wed Oct 31 18:40:45 CET 2007
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
Dr Marcin Krol
Biomolecular Modelling Laboratory
Cancer Research UK
e-mail: marcin.krol at cancer.org.uk
Department of Bioinformatics
Collegium Medicum Jagiellonian University
e-mail: mykrol at cyf-kr.edu.pl
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