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