Dear Amber Users!
I have a question regarding collective dynamics calculations using normal
mode analysis and principal components analysis made in case when 1) NMA
was performed just based on one reference structure and 2) PCA was
performed for the md trajectory where each frame has been superimposed
against that reference structure. Eventually I've found good correlations
(which means that it has the same directions) in the lowest-frequency modes
from 1) and first PCs made for 2) as was obtained by means of dot product
of both eigenvectors sets. Could someone explain me briefly why such
correlation is exist? I just know that cov.matrix (which gain information
about correlations in the atomic fluctuations in the ensemble) is
correspond to the inverse of the hessian (which is the second order
derivatives of the potential calculated for 1 structure) but I don't fully
understand physical significance of that fact.
Thanks for help,
James
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Received on Tue Feb 24 2015 - 02:30:04 PST
