AMBER Archive (2004)

Subject: Re: AMBER: ptraj analyze matrix entropy

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Wed May 05 2004 - 05:28:57 CDT

Marcin Krol schrieb:
>
> Dear All,
>
> I wonder how the entropy is calculated by ptraj analyze matrix thermo
> command. Is this obtained from a quasiharmonic analysis?

Yes, the "ptraj analyze matrix thermo" command should give identical
results to the quasih program.

> What is the
> diffrence between entropy calculated in nmode (mm_pbsa.pl script) and
> analyze matrix?

nmode does a normal mode analysis (i.e. you diagonalize a Hessian matrix
obtained from a single conformation residing at a minimum of the
potential energy surface), thus you approximate your potential energy
surface at that point by a harmonic model.

analyze matrix calculates a (mass-weighted) covariance matrix from a
trajectory, whereby the inverse of this matrix is related to a "quasi"
Hessian matrix. In this "quasiharmonic" analysis, some effects of
anharmonic terms in the potentials are included, as are e.g. solvent
effects. When calculating entropies by this approach, you need to check
the convergence of your results, though.

> Could you point me to an article describing how the
> entropy in the analyze matrix command is obtained.

A good starting point is Curr Opin Struct Biol 1994, 4, 285-290. In
particular see ref. 26 and 27 therein.

Best regards

Holger

>
> Thank you in advance
> marcin
>
> Dr Marcin Krol
> Zaklad Bioinformatyki Collegium Medicum UJ
> Kopernika 7E
> 31-501 Krakow
> tel/fax (012) 422-77-64
> e-mail mykrol_at_cyf-kr.edu.pl
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++                             
Dr. Holger Gohlke

J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Germany                         

Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29826
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.rz.uni-frankfurt.de/~hgohlke
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