[gmx-users] Correlation Matrix Calculation

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Fri Aug 31 08:57:37 CEST 2007


On Friday, 31. August 2007 05:14, Arneh Babakhani wrote:
> 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).

take a look at Generalized Correlation for Biomolecular Dynamics from Lange 
and Grubmueller:


> Much thanks,
> Arneh



 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de

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