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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