[gmx-users] frequency of modes by principal components analysis

xzp02 at mails.tsinghua.edu.cn xzp02 at mails.tsinghua.edu.cn
Sun Sep 18 05:18:54 CEST 2005

Dear All:
        I am studying modes of motion using gmx. Firstly normal modes is
calculated by g_nmeig and g_anaeig, corresponding frequency (eigenvalue) and
eigenvector is obtained. Then for dynamical case, g_covar and g_anaeig is used to
obtain the mean-square fluctuation (eigenvalue) and eigenvectors. But because the
normal modes, which is harmonic approximation on the equilibrium structure, may
not be a good representation in dynamics, so I wanna extracted the modes by PCA,
the question is I want to check the frequency of modes (that is, eigenvectors by
g_covar and g_anaeig), I think FFT on projections (obtained by g_anaeig -proj)
should work. Can anyone give some comments on it, or is there more convenient way
to do it? 
       Thanks a lot !

Xu Zhiping 
Ph.D Candicate
Department of Engineering Mechanics
Tsinghua University
Beijing, 100084, CHINA

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