[gmx-users] Constraints and Energy Minimization

[Justin Lemkul]

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
> faithfully?
>

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

-- 
==================================================

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

==================================================