Hi Tyler,<br><br>Note that the eigenvalue represents the sum of the variances for each particle along the associated eigenvector. That seems quite reasonable to me.<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 4/6/06,
<b class="gmail_sendername">Tyler Luchko</b> <<a href="mailto:tluchko@ualberta.ca">tluchko@ualberta.ca</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br><br>I have performed PCA analysis, without mass weighting, on a peptide<br>using g_covar and g_anaeig. The first principal component generally<br>corresponds to the stretching of the peptide. I understand that each
<br>eigenvalue represents the variance in the motion along the associated<br>eigenvector. However, the square root of the variance for the first<br>eigenvalue is ~20 nm while the maximum extended length of any peptide<br>
is ~3 nm. I have tried normalizing the eigenvalues by the number of<br>atoms used for the analysis (73) but this gives the standard<br>deviation of the motion to be ~2.2 nm, still much too large. I would<br>like to know how to normalize the eigenvalues to obtain reasonable
<br>standard deviations from the eigenvalues.<br><br>Thank you,<br><br>Tyler<br><br><br> ________________________________________________________________<br>(_ Tyler Luchko Ph.D. Candidate _)
<br> _) Department of Physics University of Alberta (_<br>(_ Edmonton, Alberta, Canada _)<br> _) 780-492-1063 <a href="mailto:tluchko@ualberta.ca">
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</div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands
<br>+31 50 363 4336<br>