Hi Sukesh, Great. This makes things much clearer. So basically what you'd need to do is to divide each i,j-th element of the covariance matrix you obtained (covar.dat) by the sqrt of the ii-th and jj-th diagonal element. That will commonly turn a covariance matrix into a correlation matrix. But, that also happens to be what the modified version of g_covar provided by Ran does. I think it's still on the contributions page.
Just one more thing, the generalized correlation of Lange and Grubmueller is a bit of a different thing. Might also be handy though. In stead of calculating the correlation as the normalized product moment, they have a similarity parameter that measures how close the actual distribution of measurements is to the one you'd get if the measurements were uncorrelated (mutually independent). This compensates for non-linear relationships between variables. Cheers, Tsjerk On Wed, Mar 24, 2010 at 7:16 AM, 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 > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php