Dear Jonathan - Is it not a PBC effect? Try to display atoms as spheres - it will look better. Otherwise, use the options in trjconv to remove PBC in the visualized structure(s).
Dr. Vitaly V. Chaban On Mon, Sep 23, 2013 at 9:22 AM, Jonathan Saboury <jsab...@gmail.com> wrote: > I tried minimizing a box of cyclohexanes and water. The first frame is > fine, but after that seemingly random lines form in vmd with the > cyclohexanes. The waters seem to minimizing just fine though. > > I am sure I am just doing something extremely silly and I just don't know > it because of ignorance. I have no formal training on simulations, you are > my only hope! > > Perhaps using the em.gro with the em.trr is not the correct way to > visualize? I used the command: "vmd em.gro em.trr" > > Or something is wrong with my em.mdp? > em.mdp: http://pastebin.com/raw.php?i=LPPN5xRF > > Commands used: http://pastebin.com/raw.php?i=Jk0fKLJj > Here are all the files, in case you need them: > http://www.sendspace.com/file/gx8j97 > > Sorry for dumping all of this, but I am genuinely stuck. I've tried reading > about the mdp file format but i only understand ~5%. If I could have done > more I would have tried :/ > > Thank you all, it is really appreciated. > > -Jonathan Saboury > -- > 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
