[gmx-users] PCA eigenvalue normalization

[Tsjerk Wassenaar]

Hi Tyler,

Note that the eigenvalue represents the sum of the variances for each
particle along the associated eigenvector. That seems quite reasonable to
me.

Tsjerk

On 4/6/06, Tyler Luchko <tluchko at ualberta.ca> wrote:
>
> Hello,
>
> I have performed PCA analysis, without mass weighting, on a peptide
> using g_covar and g_anaeig.  The first principal component generally
> corresponds to the stretching of the peptide.  I understand that each
> eigenvalue represents the variance in the motion along the associated
> eigenvector.  However, the square root of the variance for the first
> eigenvalue is ~20 nm while the maximum extended length of any peptide
> is ~3 nm.  I have tried normalizing the eigenvalues by the number of
> atoms used for the analysis (73) but this gives the standard
> deviation of the motion to be ~2.2 nm, still much too large.  I would
> like to know how to normalize the eigenvalues to obtain reasonable
> standard deviations from the eigenvalues.
>
> Thank you,
>
> Tyler
>
>
>   ________________________________________________________________
> (_    Tyler Luchko                           Ph.D. Candidate    _)
>   _)   Department of Physics            University of Alberta   (_
> (_    Edmonton, Alberta, Canada                                 _)
>   _)   780-492-1063                       tluchko at ualberta.ca   (_
> (________________________________________________________________)
>
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060406/0ffa9560/attachment.html>