[gmx-users] carbon nanotube - ifnite in length ?
s.neumann08 at gmail.com
Thu Oct 10 15:34:32 CEST 2013
Thanks a lot. You the bond as a distance between atoms? I wish to avoid
bonds as they are not necessary...just position restraint. What would be
the force constant? I tried 1000 once without bonds and my atoms were
moving a bit...
On Thu, Oct 10, 2013 at 2:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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.
> 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 <jalemkul at outerbanks.umaryland.edu> | (410)
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