Hi Kavya, > Thanks sir. I will go through them. However I have referred - > "A Tutorial on Principle component Analysis" by Lindsay I Smith. > Which gave a good understanding about the concepts. Still I > have some doubts regarding eigen values, as you have told > I will think over them again.
I know that one :) I'd advise others thinking of using PCA in MD to also read it... It also pays off to read a few more, though, to get slightly different viewing angles and to get used to different ways of telling the same story. > But one statement I was not clear from your previous mail that - > "An eigenvalue is an RMSF of the collective motion." I shouldn't have said RMSF, as it's not the root. The first eigenvalue is the variance or mean square fluctuation of the projection of your data onto the first eigenvector. > > These eigenvalues are the solutions for an Nth order equation > arising from N X N covar (sorry for using this term again) matrix > (considering only x component). If we consider this covar matrix > as a transformation matrix, eigen value would give the magnitude > and direction by which the eigenvector is transformed linearly. > Is it correct? No, the matrix of eigenvectors is a transformation (rotation) matrix. The eigenvectors in a sense give the directions of motion, and the eigenvalues the magnitudes. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials 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/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. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
