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 <[email protected]> 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 > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > >
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