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
