Re: [AMBER] PCA analysis for side chain atoms and backbone atoms

From: case <>
Date: Wed, 26 Jan 2011 09:43:49 -0500

On Wed, Jan 26, 2011, Jorgen Simonsen wrote:
> Without translations and rotations included (and hence 6 degrees of
> freedom removed) you should actually get six modes with frequencies
> close to zero. In practice, however, I have seen similar figures as
> yours. I suppose the other N - 6 modes look "fine". I am not sure
> what is going on here.

When you remove translations and rotations, the system thinks there is an
enormous force preventing such motions from taking place, and hence thinks
the vibrational frequency along such modes is arbitrarily large, not zero (as
they would be for true normal mode analysis, where there is no change in
energy upon translation or rotation.) So, if the other modes look fine, you
can ignore the final 6.

PCA analysis should give more informative messages here, and volunteers from
the development team are hereby encouraged to look into this.


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Received on Wed Jan 26 2011 - 07:00:09 PST
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