Re: AMBER: Correlation matrix used in quasih (Amber 7)

From: David A. Case <>
Date: Thu, 18 May 2006 05:31:00 -0700

On Thu, May 18, 2006, Craig Gough wrote:
> I would like to access directly the elements of the fluctuation
> covariance matrix used in quasih (AMBER 7), to examine correlated
> motions in a protein (without reference to any particular mode). Would
> someone tell me the appropriate variables and portions of the quasih.f
> code (or related modeles) to use? I could be brave and attempt to do
> this myself, but to avoid interpreting the code incorrectly, I would
> prefer to ask first.

Quasih doesn't construct the covariance matrix explicitly. I think it would
be the matrix product of "a" times "aT" (probably divided by the number of
snapshots to get normalized covariances). The code is pretty straightforward,
so don't be shy about trying to grok it.

....good luck...dac

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Received on Sun May 21 2006 - 06:07:08 PDT
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