[gmx-users] Correlation Matrix Calculation

Arneh Babakhani ababakha at mccammon.ucsd.edu
Fri Aug 31 05:14:17 CEST 2007

Can anyone briefly recommend a procedure for calculating the correlation
matrix (not the diagonalized covariance matrix, as done by g_covar) of a
specified group?

In particular, I'm looking to calculate the covariance matrix, as specifed
in the Karplus paper (Proteins: Vol 11:205-217, 1991), where each entry of
the matrix is defined as the correlation between the i-th and j-th atom:

c_ij = <delta r_i> <delta r_j>

where delta r is the deviation of i from its average position, averaged
over the ensemble.

Or, is there a way to use g_covar and suppress the diagonalization step,
so as to obtain only the translation correlation matrix??? (I couldn't
find anything to this effect in the manual).

Much thanks,


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