[gmx-users] None constraints and l-bfgs.

[Justin Lemkul]

On 7/29/15 7:30 AM, Dawid das wrote:
> Dear Gromacs Experts,
>
> I am trying to run l-bfgs minimization with following options (apart from
> others):
>
> integrator               = l-bfgs ; (other: cg, l-bfgs)
> constraints              = none ; no constraints
>
> but I still get a message that l-bfgs does not work with constraints so I
> should either change to cg or steep (which work) or remove constraints.
> Aren't my constraints removed with the keyword above? I also use restraints
> but this is a different case, isn't it?
>

It has nothing to do with restraints.  If you have water molecules, they are 
constrained with SETTLE by default.  To turn that off you would need "define = 
-DFLEXIBLE" but you should subsequently re-minimize with constraints to avoid 
weird geometries.

-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

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