[gmx-users] cross correlations

Fri Jun 24 15:27:20 CEST 2011

Hello,
I have some doubts regarding the output file correl.dat as it contains 3
columns, but I am not able to get what are
these column contains,I mean how to change it to the format in which I can
directly plot the data to get DCCM map...
For e.g in this form
Res1  Res2  Correlation coefficient
x         y        z
On Sun, Jun 19, 2011 at 16:16, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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
> <alexxy at 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
> >> <alexxy at 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:   korkmaz at wisc.edu [1]
> >>>>
> >>>>
> >>>>
> >>>> Links:
> >>>> ------
> >>>> [1] mailto:korkmaz at 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:alexxyum at gmail.com
> >>> mailto:alexxy at gentoo.org
> >>> mailto:alexxy at omrb.pnpi.spb.ru
> >>> --
> >>> gmx-users mailing list    gmx-users at 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-request at 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:alexxyum at gmail.com
> > mailto:alexxy at gentoo.org
> > mailto:alexxy at omrb.pnpi.spb.ru
> > --
> > gmx-users mailing list    gmx-users at 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-request at 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 at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>

-- 
-----------------------
*Regards,*
Bipin Singh
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110624/0e7f53d8/attachment.html>