On 2/2/14, 11:29 AM, Xu Dong Huang wrote:
Dear all, I am unclear about the bond exclusion properties within gromacs. Using a martini model system, what is the default behavior of setting [moleculetype] ;name exclusions eth 1 exclusions to 1? How do I find out what kind of interaction it is excluding? I am interested in finding out if this is excluding 1-3 interaction or 1-4 interaction. I guess what I also want to know is if my settings are including 1-4 bonded interactions or using only 1-3.
The value of nrexcl is the number of bonded neighbors that are excluded from nonbonded interactions. With nrexcl = 1, only 1-2 interactions are excluded; 1-3 and 1-4 interactions are calculated as normal nonbonded interactions.
-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 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.
