[gmx-users] Regarding the construction of Dynamics cross correlation map from covar.dat(from g_covar)

bipin singh bipinelmat at gmail.com
Wed Mar 23 11:18:52 CET 2011

Hello users,

Although there was already much discussion had been done on the procedure to
construct DCCM map from covar.dat(i.e. output from g_covar) but still I am
not clear
with the step wise procedure to calculate the correlation matrix from
covarience matrix(covar.dat).

1) It is stated in the previous posts that to calculate correlation matrix
we have to
divide each i,j-th element of the covariance matrix (covar.dat) by the sqrt
of the ii-th and jj-th diagonal
element, but how to get diagonal of a 865107X3 matrix???
2) As given in the manual the order of elements in covar.dat is is:
x1x1,x1y1, x1z1, x1x2, ...
But I am not clear which are i,j-th ,ii-th and jj-th elements in covar.dat.

My covarience matrix have  865107 rows and 3 columns and the total atoms are
537(sqrt( 865107 X 3) / 3=537 atoms)
Can anyone suggest how to transform the covar.dat into correlation matrix.
I am expecting the stepwise procedure to construct the correlation matrix
and not the theory behind it as it already stated in the
previous posts.

Bipin Singh
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110323/12f6df13/attachment.html>

More information about the gromacs.org_gmx-users mailing list