[gmx-users] bond constraints: which distance is constrained?

[Justin Lemkul]

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

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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
http://mackerell.umaryland.edu/~jalemkul

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