[gmx-users] PCA eigenvalue normalization

Tyler Luchko tluchko at ualberta.ca
Thu Apr 6 03:26:10 CEST 2006


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 Luchko                           Ph.D. Candidate    _)
  _)   Department of Physics            University of Alberta   (_
(_    Edmonton, Alberta, Canada                                 _)
  _)   780-492-1063                       tluchko at ualberta.ca   (_

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