[gmx-users] Bond interaction exclusions
jalemkul at vt.edu
Sun Feb 2 17:34:05 CET 2014
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
> ;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 A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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