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,
Ran
On Wed, 24 Mar 2010 11:46:42 +0530
sukesh chandra gain <suk...@atc.tcs.com> wrote:
Hi Tsjerk,
Thank you for your reply. May be I was not very clear with my previous
post.
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/102/4/994/F2.large.jpg,
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
(http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/GeneralizedCorrelations/index.html)
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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