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 > _______________________________________________ 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
