[gmx-users] Dynamics cross correlation map

Ran Friedman, Biochemisches Inst. r.friedman at bioc.uzh.ch
Wed Mar 24 07:44:16 CET 2010

Hi Sukesh,

I once put a version of g_covar that can calculate the correlations in the 
user contributions. Check if it's there or reply to me privately if you 
can't find it (though I'm on the road till Friday).

Good luck,

On Wed, 24 Mar 2010 11:46:42 +0530
  sukesh chandra gain <sukesh at atc.tcs.com> wrote:
> Hi Tsjerk,
> Thank you for your reply. May be I was not very clear with my previous 
> I am not looking for covariance / atomic covariances map (ie., 
>covar.xpm/covara.xpm) which are generated by g_covar tool in GROMACS. I am 
>particularly trying to get correlation map (example: 
>http://www.pnas.org/content/99/26/16597/F3.small.gif). I hope there is a 
>difference between covariance matrix and correlation matrix.
> The correlated motions between two atoms is calculated as the magnitude of 
>the co-relation coefficient between the atoms.  In case of a system it can 
>be assessed by examining the magnitude of all pairwise cross-correlation 
>coefficients. The cross-correlation coefficient, C(i,j) for each pair of 
>atoms i and j is calculated as:
> C(i,j) = < delta r(i) * delta r(j) > / sqrt < sqr(delta r(i) ) > . sqrt < 
>sqr(delta r(j) ) > , where delta r(i) is the displacement from mean 
>position of the ith atom and < > symbol represents the time average.
> This function returns a matrix of all atom-wise cross-correlations whose 
>elements, C(i,j), may be displayed in a graphical representation frequently 
>termed a dynamical cross-correlation map, or DCCM. If C(i,j) = 1 the 
>fluctuations of atoms i and j are completely correlated, if C(i,j) = -1 the 
>fluctuations of atoms i and j are completely anticorrelated and if C(i,j) = 
>0 the fluctuations of i and j are not correlated.
> Now my query is there any tool like g_correlation 
>by which I can get the cross-correlation matrix from covariance matrix or 
>directly from trajectory file.
> Ref:1. Hünenberger PH, Mark AE, van Gunsteren WF; Fluctuation and 
>cross-correlation analysis of protein motions observed in nanosecond 
>molecular dynamics simulations; JMB 1995; 252:492-503
> 2. Oliver F. Lange, H. Grubmüller; Generalized Correlation for 
>Biomolecular Dynamics; Proteins  2006; 62:1053-1061
> Thank You,
> Regards,
> Sukesh
> -- 
> Sukesh Chandra Gain
> TCS Innovation Labs
> Tata Consultancy Services Ltd.
> 'Deccan Park', Madhapur
> Hyderabad 500081
> Phone:  +91 40 6667 3572
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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Institute of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Skype: ran.friedman

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