[gmx-users] freezing or constraining

[Justin Lemkul]

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 
movement.

-Justin

> 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
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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