Hi Pawan, This goes beyond a few lines of explanation. Move away from the tools g_covar and g_anaeig slowly ;) and do some more background reading on principal component analysis. I've tried to explain it in my tutorial at http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html (which will probably answer your questions) and there are many documents on the internet describing PCA as a statistical tool.
Cheers, Tsjerk On Tue, Aug 17, 2010 at 9:56 AM, pawan raghav <pwnr...@gmail.com> wrote: > Hi all, > > I have a confusion regarding "Essential Dynamics". I have read so many > papers regarding PCA and ED most of the papers among them explained > eigenvectors and eigenvalues are as follows: > > if a protein has 207 C alpha residues then the total no of eigenvectors are > 3N X 3N, where N= no. of atoms i.e. 3 X 207 = 621 eigenvectors. is it means > that an eigenvector represents an C-alpha residue? > > But manual described that representations the direction of motions. > > But 3N X 3N is a covariance matrix that means this represents 621 X 621 > eigenvectors is it true? > > Then when we plot a 2dproj.xvg file between eigenvector 1 and eigenvector 2, > is it mean to plot a 2d graph between first two C-alpha atoms or first two > structures? > > Please clearify me where I was wrong. > > The 2d graph shows oval and random large trajectory graph which represents > the independent and dependent motion, may I know what does it mean? > > -- > Pawan > -- > 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/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. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands -- 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/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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
