[gmx-users] Constraints and Energy Minimization
jalemkul at vt.edu
Sun Apr 26 04:28:04 CEST 2015
On 4/25/15 10:25 PM, Eric Smoll wrote:
> Hello Gromacs Users,
> I am studying a forcefield where certain bond force constants were not
> specified because the associated bond lengths were "constrained." What do I
> need to do to run a simulation that is consistent with the way this
> forcefield was designed? Will LINCS constraints satisfy this requirement
Specify [constraints] in the topology with the correct length. LINCS will
satisfy it; that's what it was designed to do.
> In a molecular dynamics workflow, when are constraints best introduced? For
> example, should constraints be used during energy minimization?
Sounds like your force field requires it, so there's really no question.
In general, I say if you're going to run the MD with constraints, you need to
minimize with constraints. All too often I have seen bad geometries come from
unconstrained EM, which upon starting MD with constraints, cause failure. An
initial EM without constraints may be needed if the initial geometry is really
bad, but a subsequent constrained minimization is a good idea in that case.
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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