[gmx-users] Figures of PCA analysis

[Dallas Warren]

Which papers have you read so far?

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Ahmet yildirim
> Sent: Monday, 15 July 2013 9:41 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Figures of PCA analysis
> 
> 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?
> > --
> > Ahmet Yıldırım
> > --
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> 
> 
> --
> Ahmet Yıldırım
> --
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