[gmx-users] freezing or constraining

Justin Lemkul jalemkul at vt.edu
Wed Jul 4 23:55:23 CEST 2018

On 7/4/18 5:52 PM, Dallas Warren wrote:
> Freezing means that the atoms are not able to move.
> Constrained means that the atoms can move around a certain point,
> there is some movement possible.

Not quite - though historically people have used "constrain" and 
"restrain" interchangeably, that's not the case. A "constraint" strictly 
refers to the fixing of a bonded interaction, whereas a "restraint" is 
what you're talking about - a harmonic biasing potential that disfavors 


> Catch ya,
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
> On Tue, 3 Jul 2018 at 23:51, Alex <alexanderwien2k at gmail.com> wrote:
>> Dear all,
>> In studying the solid surfaces, I have noticed that some people freeze or
>> constrain the slab's atoms to their initial or relaxed coordinates, I was
>> wondering if doing that is a proper approach? If it is, where the penalty
>> energy of being frozen or constrained goes?
>> I can understand that freezing the middle atomic layers to mimic the bulky
>> behaviors is acceptable to some extent not the whole slab!
>> Also, what is the difference between freezing and constraining in this
>> issue?
>> Thanks,
>> Alex
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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