[gmx-users] Correlation Matrix Calculation
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
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).
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