[gmx-users] bond constraints: which distance is constrained?
jalemkul at vt.edu
Wed Dec 16 14:33:25 CET 2015
On 12/16/15 8:29 AM, Vitaly V. Chaban wrote:
> In bond constraints (all-bonds; LINCS...), does it constrain an initial
> bond length (as in GRO) or an equilibrium bond length (as in ITP)?
> My tests reveal the constrained distance is taken from ITP, which is
> somehow counter-intuitive to me.
The constraint length is the equilibrium bond length as specified in the
topology. It's the same thing with applying a bond potential; the reference
value is taken from the force field, not the geometry you supply. Constraints
convert those bonds (with specified equilibrium length) to a rigid entity.
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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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