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
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--
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
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