[gmx-users] On the collective dynamics in terms of NMA and PCA

James Starlight jmsstarlight at gmail.com
Tue Feb 24 11:20:48 CET 2015

Dear Gromacs Users!

I have a question regarding calculation of the collective dynamics 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 is correspond to the
inverse of the hessian but I don't understand physical meaning of that fact.

Thanks for help,


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