On 7/29/15 2:32 AM, James Lord wrote:
Hi all, I have made an oil slab (energy minimized, equilibrated nvt and npt), some of the oil molecules are at the other end (periodicity). https://drive.google.com/open?id=0B0YMTXH1gmQsYmdvQ3huYWtDaGs then I decided to increase the box size in z direction a bit to make enough room for protein, using editconf -f OCT_npt.gro -oOCT_newbox.gro -box 6.47271 6.47271 16 -noc https://drive.google.com/open?id=0B0YMTXH1gmQsT1M3dzBNNTJrT28 I used the last flag to put the oil at the ends of box but it is not doing for one end? any thoughts?
You have broken molecules. Make them whole with trjconv before resizing the box. Note that with -noc, your slab will always be on one "end" of the box, but the distinction between "ends" is irrelevant with periodicity.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
