[gmx-users] Correlation Matrix Calculation

[Tsjerk Wassenaar]

Hi Arneh,

You're not clear on what you want. Is it a covariance matrix or a
correlation matrix. Correlation and covariance are different things.
g_covar lets you write out a covariance matrix using the option
-ascii. In case you want the correlation matrix (though IIRC Karplus
also used the covariance matrix), you have to divide each element m_ij
by sqrt(m_ii)*sqrt(m_jj).

Cheers,

Tsjerk

On 8/31/07, Arneh Babakhani <ababakha at mccammon.ucsd.edu> 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).
>
> Much thanks,
>
> Arneh
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623