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" <ahmedo...@gmail.com>
An: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Betreff: [gmx-users] Figures of PCA analysis
Von: "Ahmet yıldırım" <ahmedo...@gmail.com>
An: "Discussion list for GROMACS users" <gmx-users@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?
--
Ahmet Yıldırım
--
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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?
--
Ahmet Yıldırım
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
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