[gmx-users] carbon nanotube - ifnite in length ?
s.neumann08 at gmail.com
Thu Oct 10 15:54:40 CEST 2013
Thank you. I do not have any explicit solvent in my system. I included the
solvent in nonbonded parameters so not even implicit.
On Thu, Oct 10, 2013 at 2:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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 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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