On Wed, Dec 11, 2013 at 3:39 AM, Atila Petrosian <atila.petros...@gmail.com>wrote:
> Dear Justin > > Thanks for your reply. > > After energy minimization, all carbon atoms are in true position, > inside box but again, both ends of cnt were deformed, same problem I > had before I add bond length to the length of CNT in z dimension of box. > > You mentioned " possibly poor input geometry ". Please tell me how to > obtain better input geometry. > > Well, you haven't said how you're building the CNT, so there's nothing I can suggest. It was just sort of a random guess, anyway - initial coordinates being bad (for whatever reason) is one common source of instability. > I confused. How to solve this problems? > It's also possible that your force field is bad or that the box is still incorrectly sized, depending on the geometry of the CNT. -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.