[gmx-users] bond constraints: which distance is constrained?
Vitaly V. Chaban
vvchaban at gmail.com
Wed Dec 16 14:37:20 CET 2015
On Wed, Dec 16, 2015 at 11:33 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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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