[gmx-users] anomalous eigenvector in PCA (Principal Component Analysis)

[Nima Soltani]

Hi
I have performed principal component analysis by using g_covar module of
Gromacs 5.0  (Peptide's backbone atoms were selected both for least square
fit and covariance analysis)
then 2 extreme conformations along different eigenvectors derived by
"g_anaeig -extr "
The resulting structure look likes this :
https://app.box.com/s/e6b87ar9j75q227qe6sx1udeyqdszgdl
​Is there any way to correct those artifices that can be observed in the
peptide backbone?
thanks in advance for any help or guidance  ​

Best Regards,
Nima Soltani
----------------------------------------------------------
Graduate Student of Physical Chemistry
Department of Chemistry,
Sharif University of Technology.
=================================