Hi Tsjerk, yes I did make a mistake in the group that I chose . . . should be C-alpha. Anyway, thanks for the help, appreciate it,
Arneh > 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 > _______________________________________________ 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
