On Tue, Jul 2, 2013 at 11:36 AM, Pavithra <meetpavithra...@gmail.com> wrote:
> Dear gromacs users, > > I'm new to simulation. > I'm running a membrane protein simulation with gromacs and am following > KALP tutorial. > I skipped inflategro and used g_membed command to insert my protein complex > into POPE membrane. > I followed the tutorial and got the work done but with a peculiar error. > few amino acid's atoms were protruding above the box were sliced and been > added to the other side of the box.. > is this possible?. > Not only is it possible, it is expected. What you've described is the fact that your box is of insufficient size to accommodate your protein. As a consequence, PBC re-wraps the image of the protein such that it is within the unit cell (since there is no such thing as "inside" or "outside" an infinite system. > since its the first time I don't know want information I have to provide. > Please let me know if I have to send the mdp file or the command i've used. > When reporting problems, in general, such information is absolutely necessary. In this case, probably not. -Justin -- ========================================== Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ========================================== -- 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
