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 <[EMAIL PROTECTED]> 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 [EMAIL PROTECTED] (_
(________________________________________________________________)
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--
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
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