Hi Vijaya, Well, to start with that will be something as calculating the 'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoting the ith atom of the conformation x and the reference structure r and the sum is over time/observations. In the case of no variation in xi, the value you get will still be finite, in stead of zero, as would probably be most meaningful. Now for the covariances, there's a bit more to it. The covariance is the product moment of the deviations: sum((xi-ri)(xj-rj))/N. When there is no correlation, the deviations about the mean are random and average out to zero. But with the deviations against a reference, that is not the case. So the results should be regarded meaningless, unless you have a good reason for doing so, and come with a solid justification. Okay, there may be a purpose, but I'll leave that to your imagination :)
Hope it helps, Tsjerk On Thu, Mar 18, 2010 at 5:33 PM, vijaya subramanian <vijay...@hotmail.com> wrote: > Hi > Has anyone studied the effect of using different reference structures, > not the average structure, when carrying out PCA. Does it make sense to use > a structure besides the average to calculate the covariance matrix? > Thanks > Vijaya > > > > ________________________________ > Hotmail: Trusted email with powerful SPAM protection. Sign up now. > -- > 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/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