[gmx-users] eigenvalues

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jan 9 14:20:04 CET 2009

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

> 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.



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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