Hi Elad, You can't count on operations that involve PBC after fitting. In your case, you can use
trjconv -fit translation to remove translational degrees of freedom only, keeping the system consistent with PBC. Hope it helps, Tsjerk On Sun, Dec 6, 2009 at 8:50 PM, <el...@post.tau.ac.il> wrote: > Hi Tsjerk, > thanks for the reply. > > Will the MSD of the molecule also be affected by the fitting. > I'm trying to calculate the relative diffusion coefficient of an ion near a > protein. For this I thought to first fix the system according to the protein > and then calculate the msd of the ion. > I noticed in the g_msd code that periodicity is taken into account (as > expected). However, in g_msd the interest of the periodicity handling > regards regards the atom position relative to itself in previous frames. > Will this relative movement (of the atom in relation to itself in the > previous frame) be kept after doing "trjconv -fit". > > Thanks. > >> >> Hi Elad, >> >> This has been mentioned several times before, in a different context. >> But fitting only affects coordinates, and not the PBC. So after >> fitting the coordinates and the PBC don't match any more and any >> analysis requiring PBC, such as calculating minimal distances, will >> give garbled results. Always do such things on untransformed >> trajectories. >> >> Cheers, >> >> Tsjerk >> >> On Fri, Dec 4, 2009 at 7:43 PM, <el...@post.tau.ac.il> wrote: >>> >>> Hi all, >>> >>> I have a system of protein+water+ions. >>> I measured the minimum distance between one of the ions to the protein. >>> >>> Afterwards I fitted the trajectory using g_trjconv -fit rot+trans >>> >>> Did the same mindist again and the graphs are not always identical. >>> >>> Any suggestions? >>> >>> I use gromacs 4.0.5 with an octahedron box. >>> same problem happens when I do trjconv -fit rot but does not happen when >>> -fit trans. >>> >>> In VMD I do see a difference in the position of the ion relative to the >>> protein. >>> >>> Thanks. >>> Elad P. >>> > > > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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/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/mailing_lists/users.php
