VMD might do what you want with the PBC tools plugin (installed by default). http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/ unwrap being the equivalent of -nojump
Otherwise, couldn't you just view your 2 trajectories simultaneously, one with protein the other not? -Trayder On Wed, Jul 10, 2013 at 9:13 AM, Bin Liu <fdusuperstr...@gmail.com> wrote: > Hi All, > > For the convenience of visualization, I need to remove the jump of one > component (say a protein) of the system at the boundary. I don't need to, > or say I need not to remove the jump of the other components (say a lipid > bilayer), since otherwise the system will look falling apart. I noticed I > can cluster a part of a system, then output all the atoms in the system in > which only the part is clustered, and the other components unchanged. Does > GROMACS have similar function when *-nojump* is used? > > If this can not be accomplished directly, is there a way to circumvent it? > I figured out a way, but haven't implemented it. I can plug the coordinates > of the protein treated with *-nojump* into the trajectory of the whole > system which is not treated with *-nojump*. It is kind of substituting the > coordinates of one component in one trajectory with the coordinates of the > same component in another trajectory. Is there anyone aware of a tool or a > script to do this job? > > Thank you very much. > > Regards > > Bin > -- > 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
