AMBER Archive (2004)

Subject: Re: AMBER: entropy implementation in ptraj

From: David A. Case (case_at_scripps.edu)
Date: Wed Dec 15 2004 - 12:07:50 CST

On Tue, Dec 14, 2004, Raik Gr?nberg wrote:

>
> 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.

Without knowing more about which ptraj commands you used, it's hard to answer
this question. It sounds like you are going along a path that diagonalizes
the mass-weighted covariance matrix, to get quasiharmonic modes. In this
case, the entropy is calculated per mode, using quantum formulas that would be
used for normal modes. (There are faster ways that involve calculating on the
determinant, rather than the eigenvalues, but as far as I know, these are not
implemented in ptraj.)
>
>
> Next question - in ptraj, the entropy contributions from the decreasing eigen
> values neatly converge to zero.

I guess I would have to see part of the output you are referring to. The
entropy contribution should go to zero for *increasing* frequencies. Note
that with the quasiharmonic approach, it can be very difficult to get a
converged result for the entropy; see, e.g. Fig. 2 in

%A H. Gohlke
%A D.A. Case
%T Converging Free Energy Estimates: MM-PB(GB)SA Studies on the
Protein-Protein Complex Ras-Raf
%J J. Comput. Chem.
%V 25
%P 238-250
%D 2004

and references therein.

...good luck...dac

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