[gmx-users] carbon nanotube - ifnite in length ?

[Justin Lemkul]

On 10/10/13 9:44 AM, Steven Neumann wrote:
> Thanks. I will place them then within the distance from the box edge =
> distance between atoms within the tube right? I can create bonds and use
> harmonic spring constant like for backbone protein atoms...but whats the
> point when they do not move anyway? I am using NVT.
>

If your goal is simply to have some series of atoms in a cylindrical overall 
shape that do not move, there is no purpose to using bonds.  NVT will still 
suffer from problems with frozen groups; the temperature will not be right 
because after a collision with a solvent atom, the tube atom by definition 
cannot move.

-Justin

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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

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