On 12/19/13 6:14 PM, rdwducl wrote:
Thanks for the reply Justin but I'm confused. Why must the atoms be bonded? Ultimately I plan to model micellisation whereby surfactants, which only interact with each other via non-bonded terms, are driven to aggregate by this nonpolar term...
I'm making a somewhat educated guess based on what you're observing. A trivially simple test is to run two calculations with two particles in a box - one in which a bond is defined between them, and one in which there is no bond, but the atoms are at the same distance. If the results are different, my suspicion is confirmed (that the topology controls whether or not two atoms impact one another's surface accessibility).
Give that a try and see what happens. -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.
