[gmx-users] eigenvalues

[Monika Sharma]

Hi Tsjerk,
Thank you very much for correcting me. And yes that is variance, not the
literal "motion".
Regards,
Monika

On Fri, Jan 9, 2009 at 6:50 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Monika,
>
> > As far as I know, PCA analysis breaks your total motion in system, or
> rather
> > decouples it into respective motions.
>
> Well, formally, PCA tries to provide an explanation of the total
> variance in the system, in terms of a set of new, linearly unrelated
> variables.
>
> > And by the eigenvectors and the
> > corresponding eigenvalues it means that this 1st vector or the 2nd vector
> > contributes this percent of the total motion.
>
> Variance is not motion. I can be running small circles, being very
> motile, but having a small variance. I can also steadily go from one
> place to another. Though I don't need to be very active, there'll be a
> large variance in my position. So the variance is more linked to the
> range of conformations and the extent of the conformational space
> accessible than of the motility. Only if you can be  sure that there's
> no trend - no going from one place to the other - but periodic motions
> (running circles), you can say the variance is a measure of motility.
>
> > It is system-dependent. Is
> > this really related to the difference in the degrees of freedom of two
> > different systems (that I am a bit skeptic about) with which you are
> > confusing it now.
>
> No, not of different systems, but of the same (very similar) system(s)
> under different conditions, each in equilibrium, yes.
>
> Cheers,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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