[gmx-users] Eigenvector and eigenvalues

Ankita naithani ankitanaithani at gmail.com
Thu Jun 6 15:44:23 CEST 2013


I wanted to know about the eigenvectors and eigenvalues. I recently
performed the principal component analysis (only the backbone into
consideration) on a trajectory of 2000 residues. I obtained 15641
eigenvectors and 17928 eigenvalues. There is a difference in the number,
which I am not quite sure off (perhaps that has to do with eigenvalue for
each eigenvector, and the eigenvector has 3 co-ordinates x,y,z. I know I
may be wrong completely but since there are 15641 eigenvectors, then
shouldn't there by only 15641 eigenvalues for those eigenvectors)

My second problem lies that I am trying to extract information or say RMSF
values for the first 10 eigenvectors (10 slowest modes) and the last 10
eigenvectors (fastest modes) and there I face segmentation fault. I can get
information on the first 10 but when I try last 10 with the command as

g_anaeig -v eigenvec.trr -eig eigenval.xvg -rmsf eig_rmsf.xvg -first 15631

[where -first should have the starting eigenvector ]

(I choose, 15631 since I want the plot for last 10 but I get segmentation
fault, which is also to do with the fact that the eigenval.xvg has 17928
values. This number doesn't match and so, maybe the plot is from
15631-17928). This has further confused me about the slowest and fastest
modes (and somehow I do need information on the first 10 slowest modes and
10 fastest modes). In a broad way, the slowest modes would be the ones with
high eigenvalues say, first 10 eigenvectors in eigenval.xvg would give the
slowest 10 modes and the last 10 in eigenval.xvg should give the fastest 10

Here, again I feel quite confused because eigenval.xvg has 17928 entries
and in the legend, it says that x axis is the eigenvector index and y axis
is eigenvalue index so it leaves me quite perplexed about the problem.

I am sorry for this extremely long and confusing post, but any help in this
regard would be really beneficial.

Kind regards,


Ankita Naithani

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