[gmx-users] Figures of PCA analysis

[Ahmet yıldırım]

Can anybody help me understand these better?


2013/7/10 lloyd riggs <lloyd.riggs at gmx.ch>

> There vectors.  Theres some good older papers explaining the whole thing
> from Van Gunstern, Berendsen, and some other good ones from de Groot that
> explain them well and includes combining them with other data analysis
> types, but I dont remeber the actual publications.  A few are in the mid
> 1990's, however these explain PCA better than some of the newer ones...but
> some extensive reading...or text books from van guntstern and/or Berendsen
> explain the whole thing well, from the math to the actual "what it means"
> aspect.
>
> *Gesendet:* Mittwoch, 10. Juli 2013 um 14:46 Uhr
> *Von:* "Ahmet yıldırım" <ahmedo047 at gmail.com>
> *An:* "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> *Betreff:* [gmx-users] Figures of PCA analysis
> Dear users,
>
> I have a few questions about PCA analysis. I see the figures below in the
> most
> of the publications:
> 1.) Figure:Eigenvalues along the eigenvectors
> This figure gives contribution of eigenvalues along the eigenvectors to the
> overall motion of the protein???
> 2.) Figure:the projection of the MD trajectories onto the first ten
> principal components
> This figure gives contribution of the first 10 eigenvectors to the overall
> motion of the protein???
> 3.)The projection of the MD trajectories onto the plane of the first and
> the second principal components
> This figure gives knowledge about conformational spaces of structures???
>
> Which one gives information about the motion of the structure?
> Can anyone explain to me in detail what these figure are?
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Ahmet Yıldırım