Of course you did... Though mind the brackets :) C_ij = <x_i * x_j> / sqrt ( <x_i ^2> * <x_j^2> )
The point I want to make is that you can easily take the output from g_covar -ascii and turn it into a correlation matrix. In R (r-project.org) there is even a dedicated function for it: x <- scan("covar.dat") x <- matrix(x,sqrt(length(x))) y <- cov2cor(x) write(y,"correl.dat",ncolumns=3) Cheers, Tsjerk On Sun, Jun 19, 2011 at 12:37 PM, Alexey Shvetsov <ale...@omrb.pnpi.spb.ru> wrote: > Hi, > > Thats actualy that i did here [1]. Extracting coordinate for every atom in > interesting two group and computing > > C_ij = <x_i * x_j> / sqrt ( x_i ^2 * x_j^2 ) assuming that x_i and x_j is > vectors > > > [1] > http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl > On Sun, 19 Jun 2011 12:27:53 +0200, Tsjerk Wassenaar wrote: >> >> 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 > > -- > 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