[gmx-users] deformation in cnt

[Justin Lemkul]

On 12/4/13 10:48 AM, Atila Petrosian wrote:
> Dear Justin
>
> Thanks for your reply
>
> z dimension of box is exactly equal to the length of
> the cnt axis.
>
>> The box size should be (length of CNT) + (bond length).
>
> What value is appropriate for bond length to add length of CNT?
>

Whatever the lengths of the bonds are in your model.  If it's a "normal" CNT, 
they're all the same.

> So, using freeze is not suitable for my system (neither in the em step nor
> in the nvt equilibration step)? Is my opinion true?
>

Freezing isn't useful for much of anything except the most extreme cases.

> I have a general question:
> When can I use freeze? What is difference between freeze and position
> restraint? Which of them is good for my system (cnt containing systems).
>

Position restraints introduce a biasing potential to the Hamiltonian.  Atoms can 
move, but only if they overcome an energetic penalty.  If atoms are frozen, they 
cannot move at all.  I don't know what the purpose of your simulation is, but I 
doubt you need either beyond normal restraints during equilibration of solvent.

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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