[gmx-users] carbon nanotube - ifnite in length ?
jalemkul at vt.edu
Thu Oct 10 15:28:40 CEST 2013
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 A. Lemkul, Ph.D.
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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