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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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