Hey, The method from Lange is quite a different thing. It includes non-linear correlations, which is interesting to look at for overall correlation between atoms. If the ultimate goal is to do PCA on it, then it will give you awkward components that will give you a hard time trying to interpret.
There is another way, besides using an external tool. Extract the diagonal elements and take the square root of each. Then for each element [i,j] in the matrix, divide by the elements i and j of these square roots, and you'll have yourself a correlation matrix. Hope it helps, Tsjerk On Sun, Jun 19, 2011 at 11:55 AM, Alexey Shvetsov <ale...@omrb.pnpi.spb.ru> wrote: > Hi. > > There is two possibilitys > 1. utility written by Oliver F. Lange and Helmut Grubmüller [1] that > compites > general corelation coefficients > 2. My utility that computes pearson correlation coefficients [2] > > [1] > http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.html > [2] > http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl > > > On Fri, 17 Jun 2011 00:48:01 -0500, E. Nihal Korkmaz wrote: >> >> Dear all, >> >> Is there any built in function that gives me the pairwise correlation >> of the fluctuation (unit vector between two coordinates of a residue) >> of residues (averaged over the input trajectory). I tried g_covar but >> thats not what im looking for. The result I want should be an NxN >> matrix with values ranging from -1 to 1. >> >> Thanks in advance, >> Nihal >> >> -- >> Elif Nihal Korkmaz >> >> Research Assistant >> University of Wisconsin - Biophysics >> Member of Qiang Cui & Thomas Record Labs >> 1101 University Ave, Rm. 8359 >> Madison, WI 53706 >> Phone: 608-265-3644 >> Email: kork...@wisc.edu [1] >> >> >> >> Links: >> ------ >> [1] mailto:kork...@wisc.edu > > -- > Best Regards, > Alexey 'Alexxy' Shvetsov > Petersburg Nuclear Physics Institute, Russia > Department of Molecular and Radiation Biophysics > Gentoo Team Ru > Gentoo Linux Dev > mailto:alexx...@gmail.com > mailto:ale...@gentoo.org > mailto:ale...@omrb.pnpi.spb.ru > -- > 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 > -- 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