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
