[gmx-users] Correlation Matrix Calculation

Arneh Babakhani ababakha at mccammon.ucsd.edu
Fri Aug 31 16:19:04 CEST 2007

Sorry for the confusion . I want the correlation.  So I can just use
g_covar to get the covar. matrix, and divide each term by what you stated,
to get the correlation matrix? (if I follow you correctly).


> 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
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