Hi Arneh, I think this has been covered on the mailing list before. But anyway, the number indeed refers to the atom index number, running from 1-N. You mean that you have 1934427 X 3 elements in the covar.dat file? So that corresponds to sqrt( 1934427 X 3 ) / 3 = 803 atoms. I think you made a mistake with the group you chose (Protein rather than c-alpha?). You would expect to have 90000 elements for a system of 100 atoms.
Hope it helps, Tsjerk On 9/5/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote: > Thanks Tsjerk, > > One other question, regarding the covar.dat file (the covariance matrix > that's outputted when using the -ascii flag): > > I dont' quite understand the format of it. In the manual, it states: > "The order of the elements is: x1x1, x1y1, x1z1, x1x2, ..." > > Does "1" and "2" refer to the particles in the group? I'm asking b/c my > particular covar.dat file is of dimmensions 1934427 X 3 , for a group of > about 100 atoms and a traj of 1 NS. Just trying to make sense out of it > . . . > > Thanks, > > Arneh > > > > Tsjerk Wassenaar wrote: > > 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
