Re: [AMBER] Using average frame for nmode entropy calculation?

From: David A Case <>
Date: Sun, 28 Mar 2021 16:43:20 -0400

On Sun, Mar 28, 2021, Liao wrote:
>So from what I see, is calling cpptraj and seems to be generating
>an average frame over all the selected frames, and doing the quasi-harmonic
>calculation on that single frame.

The average structure is an intermediate quantity: after is computed, the
covariance matrix is computed as sigma_ij = <(x_i - xav_i)(x_j - xav_j)>,
and the average is over all the frames you ask cpptraj to use. After that,
the average structure is discarded, and the effective forces determined from
the sigma_ij covariance matrix. Depending on the size and flexibility of
the system, quasi-harmonic results can be difficult to converge.

>I guess now I’ll try to first manually generate an average in cpptraj, and
>use that single frame as the nmode calculation input to see what I get.

This would not make good sense: the average structure is often a distorted
one, and is not "representative" of the ensemble. Try doing a normal mode
calculation on a dozen or so snapshots, and see how much variation you are
getting. Then check the results using 12 snapshots vs. using 24, etc.

Here is an old, but still revelant study of this subject:

%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


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Received on Sun Mar 28 2021 - 14:00:02 PDT
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