<br>Hi Tsjerk,<br>Thank you very much for correcting me. And yes that is variance, not the literal "motion".<br>Regards,<br>Monika<br><br><div class="gmail_quote">On Fri, Jan 9, 2009 at 6:50 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Monika,<br>
<div class="Ih2E3d"><br>
> As far as I know, PCA analysis breaks your total motion in system, or rather<br>
> decouples it into respective motions.<br>
<br>
</div>Well, formally, PCA tries to provide an explanation of the total<br>
variance in the system, in terms of a set of new, linearly unrelated<br>
variables.<br>
<div class="Ih2E3d"><br>
> And by the eigenvectors and the<br>
> corresponding eigenvalues it means that this 1st vector or the 2nd vector<br>
> contributes this percent of the total motion.<br>
<br>
</div>Variance is not motion. I can be running small circles, being very<br>
motile, but having a small variance. I can also steadily go from one<br>
place to another. Though I don't need to be very active, there'll be a<br>
large variance in my position. So the variance is more linked to the<br>
range of conformations and the extent of the conformational space<br>
accessible than of the motility. Only if you can be sure that there's<br>
no trend - no going from one place to the other - but periodic motions<br>
(running circles), you can say the variance is a measure of motility.<br>
<div class="Ih2E3d"><br>
> It is system-dependent. Is<br>
> this really related to the difference in the degrees of freedom of two<br>
> different systems (that I am a bit skeptic about) with which you are<br>
> confusing it now.<br>
<br>
</div>No, not of different systems, but of the same (very similar) system(s)<br>
under different conditions, each in equilibrium, yes.<br>
<br>
Cheers,<br>
<font color="#888888"><br>
Tsjerk<br>
</font><div class="Ih2E3d"><br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
Padualaan 8<br>
3584 CH Utrecht<br>
The Netherlands<br>
P: +31-30-2539931<br>
F: +31-30-2537623<br>
_______________________________________________<br>
</div><div><div></div><div class="Wj3C7c">gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
</div></div></blockquote></div><br>