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
