<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>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.
<div>
<div name="quote" style="margin:10px 5px 5px 10px; padding: 10px 0 10px 10px; border-left:2px solid #C3D9E5; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Mittwoch, 10. Juli 2013 um 14:46 Uhr<br/>
<b>Von:</b> "Ahmet yıldırım" <ahmedo047@gmail.com><br/>
<b>An:</b> "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
<b>Betreff:</b> [gmx-users] Figures of PCA analysis</div>
<div name="quoted-content">Dear users,<br/>
<br/>
I have a few questions about PCA analysis. I see the figures below in the most<br/>
of the publications:<br/>
1.) Figure:Eigenvalues along the eigenvectors<br/>
This figure gives contribution of eigenvalues along the eigenvectors to the<br/>
overall motion of the protein???<br/>
2.) Figure:the projection of the MD trajectories onto the first ten<br/>
principal components<br/>
This figure gives contribution of the first 10 eigenvectors to the overall<br/>
motion of the protein???<br/>
3.)The projection of the MD trajectories onto the plane of the first and<br/>
the second principal components<br/>
This figure gives knowledge about conformational spaces of structures???<br/>
<br/>
Which one gives information about the motion of the structure?<br/>
Can anyone explain to me in detail what these figure are?<br/>
--<br/>
Ahmet Yıldırım<br/>
--<br/>
gmx-users mailing list gmx-users@gromacs.org<br/>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br/>
* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br/>
* Please don't post (un)subscribe requests to the list. Use the<br/>
www interface or send it to gmx-users-request@gromacs.org.<br/>
* Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a></div>
</div>
</div>
</div></div></body></html>