AMBER Archive (2004)Subject: AMBER: entropy implementation in ptraj
From: Raik Grünberg (graik_at_web.de)
Date: Tue Dec 14 2004  11:37:18 CST
Hi there,
I have rather extensively used Amber 8 ptraj for the calculation of entropies
from MD trajectories. With some tricks here and there, things have worked out
quite well  much better (and more efficient) than what I got from my own
feeble attempts of implementing this calculation. Thanks a lot for adding
this method to ptraj!
Unfortunately, I couldn't find any reference for how exactly the entropy
estimate is implemented in ptraj. I haven't got any Fortran knowledge, so I
am pretty lost when looking at the source code.
The classic way of calculating the vibrational entropy from the eigenvalues ev
of the massweighted (?) covariance matrix C would be:
(1) S = 1/2 kb SUM( ln ev_i )
or S = 1/2 kb ln  C  [Karplus Kushick 1981]
Then there is the famous Schlitter correction (Schlitter, 1993) which adds
some term to the covariance matrix before determining the eigen values:
(2) C' = C + [ M^1 h^2 / (kb T e^2) ]
(3) S = 1/2 kb ln  C' 
(M is the diagonal vector of masses)
I suppose the latter is what you are using in ptraj, isn't it?
Next question  in ptraj, the entropy contributions from the decreasing eigen
values neatly converge to zero. In my own implementation any such convergence
was usually messed up by many low but nonzero eigen values and it was never
clear where (or if) I should cut the list. This may of course point to some
mistake on my side  Anyway, is ptraj using any trick to force the
eigenvalues to converge on zero?
Thanks a lot for any help!
Greetings,
Raik


Raik Grünberg  Bioinformatique Structurale
 Institut Pasteur
Tel: +33/1.45.68.87.37  Paris, France


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