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)
-- 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