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From: David A. Case <case.scripps.edu>

Date: Wed, 15 Dec 2004 10:07:50 -0800

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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Received on Wed Dec 15 2004 - 18:53:00 PST

Date: Wed, 15 Dec 2004 10:07:50 -0800

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

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.)

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

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Wed Dec 15 2004 - 18:53:00 PST

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