On Tue, Dec 10, 2013 at 4:02 AM, Atila Petrosian <atila.petros...@gmail.com>wrote:
> Dear Justin > > > Based on your suggestion, I added C-C bond length to z dimension of box > (before: 5.5 3.5 3.5, now: 5.5 3.5 3.6418). > > Then I used genion to neutralize system using replacing 2 water molecules > by 2 Na ions, gro file obtained from genion is strange. > > When I see this gro file by vmd, some carbon atoms of CNT leave the box. > > Figure is in the bellow link: > > https://www.dropbox.com/s/kt1xk4ps3kbxze3/cnt-pic.docx > > > What is reason of this issue? > > How to fix it? > Looks like normal PBC, but possibly poor input geometry. Does energy minimization lead to a (visually) better state? -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.