[gmx-users] Regarding the construction of Dynamics cross correlation map from covar.dat(from g_covar)
bipinelmat at gmail.com
Wed Mar 23 11:18:52 CET 2011
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
with the step wise procedure to calculate the correlation matrix from
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
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