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

[Steven Neumann]

Thank you. I do not have any explicit solvent in my system. I included the
solvent in nonbonded parameters so not even implicit.

Steven


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
>
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> Justin A. Lemkul, Ph.D.
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