[gmx-users] cross correlations

[Alexey Shvetsov]

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
>> --
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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:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru