Hi Pawan, I can add two things. First of all, the score is simply the projection of a point (conformation) onto the eigenvector. Second, extreme scores/projections, be it positive or negative, are usually most unlikely, thus corresponding to highest energy. For the lowest energies, you'd be looking for projections that occur most, thus correspond to the modus of the distribution (hence 'modal'). I hope with this, you'll have enough to hold on to work your way through. If it still eludes you, I'm sorry, but I don't think I can help you much further to sort it out. Probably the best you can do is find some texts from statistics about principal component analysis (plenty on the web), and take some simple (non-MD) exercises. If you've got the view on PCA straight, then turn back to MD. Oh, maybe the paragraph on PCA in my thesis (see http://dissertations.ub.rug.nl/FILES/faculties/science/2006/t.a.wassenaar/02_c2.pdf) may also be a useful read.
Good luck! Cheers, Tsjerk On Sun, Dec 12, 2010 at 3:40 PM, pawan raghav <pwnr...@gmail.com> wrote: > Dear tsjerk, > I am very sorry to say that your suggestions does not help but increase > confusions only. I am highly obliged if you give me clear statements about > the scores to understand this concept in depth. I have searched research > article about this concept but failed to find even an single article. > Neither Gromacs tutorial give any description about these scores, nor your > PCA tutorial. I am really interested to understand this concept so help by > giving me answers of my questions. > > eigenvector Minimum Maximum > > value time value time > > 1 -9.162661 99.0 2.682097 9450.0 > > 2 -2.728093 4695.0 3.272116 558.0 > > I got clearcut idea about this line after read your tutorial "These are the > maximum and minimum projections on the eigenvectors." > What is the meaning of this line here? "They are very unlikely to correspond > to energy minima, as minima will be modal." > If the values in second column not the energy values they are scores only. > Are scores directly corresponds to the energy minima for second column and > energy maxima for 4th column on which they are based? I have seen that in > second column there are negative values (Minimum) and in 4th column there > are positive values (Maximum). In above example along the first eigenvector, > Are -9.162661 value at time 99 ps corresponding to the structure at low > energy during the projection and the value 2.682097 score corresponds to the > maximum energy. If I am wrong then tell me, what are the criteria on which > there scores are based? > I am totally agree with your this concept and understand completely in this > line "Think of a pendulum, projecting the position on the floor." > But this statement confused me "The extreme projections actually correspond > to states of higher (potential) energy". Which extreme projection > corresponds to state of higher (potential) energy either minimum or maximum > or both of them? > Please reply me line by line so that I can understand this concept. > -- > Pawan Kumar Raghav > Bioinformatician > > -- > gmx-users mailing list gmx-us...@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 > -- 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
