Hi all, I am trying to run a simulation of a protein in a water-vacuum-water box, which simulates quite well the membrane environment. I did it some years ago in amber, but know I am trying in grommacs and got the following answer when I try to run the fist "mdp" file:
ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rvdw. Of course, I tried to use the same water box complete (no deleting the vacuum layer), and it run well. So, it is not a problem of the size, but of the fact of having some aminoacids not surrounded by water. There is any option of changing some parameter in the "mdp" file (cut-off scheme...) to avoid this problem, still keeping my protein in the water-vacuum-water layers? Thanks. -- 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
