On 3/10/16 4:44 AM, gozde ergin wrote:
Dear Justin, Thanks for your respond, I assume there is a way to apply this restraint on specific molecules. Because my system is mixed with organic and water and I would like to apply these forces on organic molecules not water?
So apply flat-bottom restraints to whatever the organic molecules are. It's not something specific to ions. You set the restraints in the molecule's topology (in its [moleculetype]), construct a reference coordinate file that defines some unphysical coordinates to be used as the center of the restraint, and that's it. I've described the process in detail before so check the archive.
-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.
