[gmx-users] PCA eigenvalue normalization

[paloureiro at biof.ufrj.br]

Have you checked if your peptide is "jumping" out of the box?

Regards.

Pedro


> 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
>
>
>  ________________________________________________________________


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