On Tue, Dec 10, 2013 at 12:31 PM, Shine A <shin...@iisertvm.ac.in> wrote:
> Sir, > > I completed a 400 ns MD simulation. But in some part of the trajectory > my protein is just out side the box I selected (triclinic). Is there any > option in gromacs to constrain my protein in box during simulation. > > No, nor is there any need to do so because there is no such thing as "inside" or "outside" of an infinite system. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- ========================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow 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 ========================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
