[gmx-users] cross correlations

[Tsjerk Wassenaar]

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
> --
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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