On 7/2/14, 6:45 PM, Chetan Mahajan wrote:
Thanks a lot, Justin. It's much clearer, but one last question: If the coordinates in sample.gro extracted from xtc trajectory using trjconv ( without any application of pbc) are unwrapped, why almost all of them happen to lie in the box, as can be seen in the following snapshot? I would expect many of them scattered in space, beyond original box? https://www.dropbox.com/sh/1za0snsw20is106/AADU7hG_CMQmtZ8iI4XGKz-va Dark blue line is the box boundary.
A central unit cell is still maintained; it's just that the molecules aren't necessarily whole.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
