Thankyou!! sir. Your answer helped a lot. Richa
On 2 July 2013 13:04, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Richa, > > >From your explanation, I understand you want to know the sum of distances > between each frame and its corresponding filtered frame. I think it makes > more sense to sum squared distances, but that's a minor detail. > The (non-mass-weighted) RMSD between two structures, written as positional > vectors in 3N dimensional space, and properly rotated is: > > RMSD(a,b) = sqrt((a-b)'(a-b)) > > In your case, the objective is comparing a frame x and the frame filtered > by a set of eigenvectors, represented as the skinny matrix P: y = PP'x > > So, because the structures were fit prior to the covariance analysis > anyway, the MSD is > > MSD = (x-PP'x)'(x-PP'x) = x'x + x'PP'PP'x - 2x'PP'x > > Because the eigenvectors are an orthonormal set, P'P = I and we get > > MSD = x'x - x'PP'x > > Now, x'x is just the radius of gyration squared of the original structure, > so you can easily get that with g_gyrate for your trajectory. x'PP'x is the > inner product of the projections of x onto the eigenvectors in P, which you > get with g_anaeig -proj. So your objective is easily reached with some > relatively cheap calls to g_gyrate/g_anaeig and a bit of scripting in awk > or python, avoiding the determination of a whole RMSD matrix, just to get > the trace. In fact, it becomes rather trivial to do this for any subset of > eigenvectors you desire. > > As for the final answer, I would sum the MSD and take the square root, > rather than summing the square roots, to get a more meaningful answer. But > it's already unclear to me what these numbers would signify to begin with. > > Hope it helps, > > Tsjerk > > > > > On Tue, Jul 2, 2013 at 8:53 AM, Gaurav Goel <gauravgoel...@gmail.com> wrote: > >> Following link might be helpful: >> http://orbeckst.github.io/GromacsWrapper/gromacs/core/fileformats/xpm.html >> >> -g >> -- >> Gaurav Goel >> Assistant Professor >> Department of Chemical Engineering >> Indian Institute of Technology, Delhi >> Hauz Khas, New Delhi 110016 >> India >> >> On 02-Jul-2013, at 10:45 AM, Richa Singh <richa.s.rathor...@gmail.com> >> wrote: >> >> > Hello users, >> > >> > I'm using g_rms to compare my actual trajectory obtained from >> > simulation with the filtered trajectory (along given set of >> > eigenvectors), this gives me an RMSD comparison matrix in xpm format >> > where the values of the plot are not clear. Is there any way which can >> > help me to get the values along the diagonal of the matrix? >> > the command that i followed is: >> > g_rms -s ref.tpr -f actual.xtc -f2 filtered.xtc -m rmsd.xpm >> > >> > I want to calculate the trace of the matrix basically. >> > >> > >> > Regards.. >> > -- >> > 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 >> >> -- >> 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. > -- > 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 -- 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
