On 7/1/14, 9:08 PM, Chetan Mahajan wrote:
Thanks, Justin. Are you saying, the coordinates in .gro file extracted from xtc trajectory are not wrapped, whereas those in the .gro file generated at the end of gromacs MD run are wrapped in the box?
Yes, unless you've manipulated the trajectory in some way with trjconv beforehand.
Now I have a question: the negative coordinates that are present in the following text are from .gro file (generated at the end of MD run), whereas positive ones are from .gro file obtained using trjconv on xtc.
Either way, it's a periodicity effect. Molecules are made 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.
