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
