Dear Tsjerk, Thanks very much. Yes, true, difference in the ranges of the covariances means there is difference between the two systems. I did try the modified g_covar in the contribution section but couldn't make it work first, but I realized it worked only for GROMACS ver 3.3.3. Now, I am able to calculate the correlation matrix.
Thanks very much for all your help and pointers. Sincerely, Vignesh On Thu, Nov 11, 2010 at 4:49 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Vignesh, > > If your covariances show different ranges, isn't that a difference > between your systems, wild-type and mutated? Then again, there's also > noise in the covariances (noise in the fluctuations, ergo noise in the > noise ;)). The rest might be comparable, making scaling based on the > extremes seem like a bad idea. You might be better of calculating > correlations, rather than covariances. There's a modified g_covar in > the contributions section of the gromacs site for calculating those. > > Cheers, > > Tsjerk > > On Thu, Nov 11, 2010 at 3:53 AM, Vigneshwar Ramakrishnan > <vmsrvign...@gmail.com> wrote: > > Dear All, > > I tried using the xpm2ps -combine option to plot the two matrices in the > > same plot. > > "xpm2ps -f covara_cognate.xpm -f2 covara_G5C.xpm -diag none -combine > halves > > -cmin -0.5 -cmax 0.8" > > > > However, I still get two legends and each of the matrices are scaled > > differently. That is, the output range is NOT combined, as the -combine > > option is supposed to do. I tried different options (add, sub, div ; with > > and without the -cmin and -cmax options etc) > > I am sure I am missing something here. May I please know if anybody got > it > > worked, and if so, can help me out? > > Thanks very much, > > Vignesh > > On Thu, Nov 11, 2010 at 10:12 AM, Vigneshwar Ramakrishnan > > <vmsrvign...@gmail.com> wrote: > >> > >> Thanks very much, Justin. Somehow this thread did not come up during my > >> search. > >> Really appreciate your help. > >> Sincerely, > >> Vignesh > >> > >> On Wed, Nov 10, 2010 at 10:23 PM, Justin A. Lemkul <jalem...@vt.edu> > >> wrote: > >>> > >>> There are two relevant threads on this same topic that will likely > >>> provide some insight (particularly the second): > >>> > >>> http://lists.gromacs.org/pipermail/gmx-users/2009-November/046846.html > >>> http://lists.gromacs.org/pipermail/gmx-users/2009-November/046854.html > >>> > >>> -Justin > >>> > >>> Vigneshwar Ramakrishnan wrote: > >>>> > >>>> Dear All, > >>>> I am trying to study the effect of single-point mutations on > correlated > >>>> motions in a protein-DNA system. I am able to calculate the atomic > >>>> covariance matrix using the g_covar -xpma option. However, when I try > to > >>>> compare the covariance matrices for the two systems (to study the > effect of > >>>> the mutation), I find that the output is not scaled identically. That > is, in > >>>> one of the systems the atomic covariance varies between -0.04 and +0.5 > >>>> whereas in the other it varies between -0.1 and +0.4. Now, this means > that I > >>>> cannot compare the two systems immediately from the eps file output > >>>> (obtained after xpm2ps). > >>>> Could anybody please tell me if there is a way to plot the output on > >>>> identical scales (say, -1 to +1, or any other scale) using GROMACS? > >>>> The other way, I understand is to use the ascii output of g_covar and > >>>> use the values to create the covariance plot using softwares like > MATLAB > >>>> which can rescale the image colors. However, for this, one needs to > >>>> calculate the atomic covariance from the ascii output (which is > >>>> x1x1,x1y1,x1z1 etc). From the manual, I understand that the way to > calculate > >>>> atomic covariance is "for each atom pair the sum of the xx, yy and zz > >>>> covariances". Am I right if I understand that this means: > >>>> atomic cov (X1) = x1x1 + y1y1 + z1z1 atomic cov (X2) = x2x2 + y2y2 + > >>>> z2z2 ... > >>>> I greatly appreciate any help or pointers. > >>>> Thanks very much, Sincerely, Vignesh > >>>> > >>>> > >>>> -- > >>>> R.Vigneshwar > >>>> Graduate Student, > >>>> Dept. of Chemical & Biomolecular Engg, > >>>> National University of Singapore, > >>>> Singapore > >>>> > >>>> "Strive for Excellence, Never be satisfied with the second Best!!" > >>>> > >>>> I arise in the morning torn between a desire to improve the world and > a > >>>> desire to enjoy the world. This makes it hard to plan the day. (E.B. > White) > >>>> > >>> > >>> -- > >>> ======================================== > >>> > >>> Justin A. Lemkul > >>> Ph.D. Candidate > >>> ICTAS Doctoral Scholar > >>> MILES-IGERT Trainee > >>> Department of Biochemistry > >>> Virginia Tech > >>> Blacksburg, VA > >>> jalemkul[at]vt.edu | (540) 231-9080 > >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >>> > >>> ======================================== > >>> -- > >>> gmx-users mailing list gmx-users@gromacs.org > >>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>> Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >>> Please don't post (un)subscribe requests to the list. Use the www > >>> interface or send it to gmx-users-requ...@gromacs.org. > >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> > >> > >> -- > >> R.Vigneshwar > >> Graduate Student, > >> Dept. of Chemical & Biomolecular Engg, > >> National University of Singapore, > >> Singapore > >> > >> "Strive for Excellence, Never be satisfied with the second Best!!" > >> > >> I arise in the morning torn between a desire to improve the world and a > >> desire to enjoy the world. This makes it hard to plan the day. (E.B. > White) > > > > > > > > -- > > R.Vigneshwar > > Graduate Student, > > Dept. of Chemical & Biomolecular Engg, > > National University of Singapore, > > Singapore > > > > "Strive for Excellence, Never be satisfied with the second Best!!" > > > > I arise in the morning torn between a desire to improve the world and a > > desire to enjoy the world. This makes it hard to plan the day. (E.B. > White) > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- R.Vigneshwar Graduate Student, Dept. of Chemical & Biomolecular Engg, National University of Singapore, Singapore "Strive for Excellence, Never be satisfied with the second Best!!" I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White)
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists