[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,
Arneh
More information about the gromacs.org_gmx-users
mailing list