Hi Arneh, Yes. As you should be able to recall, the (linear, not "generalized") correlation is formally given as:
cor(x,y) = cov(x,y) / ( sqrt(var(x))*sqrt(var(y)) ) The diagonal elements of the covariance matrix give the variances... Cheers, Tsjerk On 8/31/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote: > 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). > > Thanks, > > > 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 <[EMAIL PROTECTED]> 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 > >> > >> _______________________________________________ > >> gmx-users mailing list gmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before > >> posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > > > > > -- > > 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 > > > > -- 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
