On 6/1/15 9:07 AM, soumadwip ghosh wrote:
Hi Justin, the snapshot I uploaded in the URL is of the SSDNA-CNT system after energy minimization step not before it. I stripped off water and ions from the system for the ease of visualization. I would be grateful if you suggest me a possible way out.
I don't see how that changes what I've said. You have a topology problem with the CNT. Simplify the system - build a smaller CNT, minimize it in vacuo, etc, then make it bigger/more complex. Look at the atoms that are distorting and check the existence of their bonded interactions and associated parameters.
-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.