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

From: Hannes Loeffler <>
Date: Wed, 26 Jan 2011 15:02:49 +0000

On Wed, 26 Jan 2011 09:43:49 -0500
case <> wrote:

> 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.

The problem at the moment is that those large "modes" will be just
plugged into the formula for the entropy and will therefor lead to the

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Received on Wed Jan 26 2011 - 07:30:04 PST
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