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

[Justin Lemkul]

On 10/10/13 9:21 AM, Steven Neumann wrote:
> How about applying position restarints with a strong force constant? What
> is less computationally expensive: position restrained, freezing the whole
> molecule? The nanotube should be rigid... Shall I place the edged of the

You shouldn't see any real performance gain or loss by applying either 
restraints or freezing.

> tube on the box edge as well and use pbc=xyz and periodic molecules = yes?
>

The box size needs to be (length of tube) + (bond length).  If you place the 
carbon atoms at the box edge, they overlap and the system blows up.

-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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