AMBER Archive (2003)

Subject: Re: Quasi-harmonic analysis

From: Miyashita, Osamu (omiyashita_at_ucsd.edu)
Date: Fri Jan 31 2003 - 12:25:23 CST

I would like to have a word for the difference between quasi-harmonic
analysis (QHA) and principal component analysis (PCA).

> They only differ in minor ways: in quasiharmonic analysis, the coordinates
> are mass weighted, whereas in PCA they are not.

Maybe it is general opinion, but I have seen some papers with mass-weighted
PCA, ex

Nolde, S. B., Arseniev, A. S., Orekhov, V. Y. & Billeter, M. Essential
domain motions in barnase revealed by MD simulations. Proteins 46, 250-8
(2002).
Kitao, A. & Go, N. Investigating protein dynamics in collective coordinate
space. Curr Opin Struct Biol 9, 164-9 (1999).

Some papers call 'not mass weighted PCA analysis' as 'essential dynamics'.

I think, PCA is a general word for statistical analysis. It can be done with
or without mass weighted. Difference is only that the mass weighted analysis
can be compared to normal mode analysis, since it's eigenvalues are related
to frequency, but the non-mass-weighted analysis cannot be.

Miyashita, Osamu
Department of Physics
University of California at San Diego
email: omiyashita_at_ucsd.edu