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

[Steven Neumann]

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.

Steven


On Thu, Oct 10, 2013 at 2:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/10/13 9:34 AM, Steven Neumann wrote:
>
>> 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...
>>
>>
> If you don't have bonds, then there is no point using periodic_molecules.
> Still, the point stands that you cannot place atoms at the box edge,
> because they will overlap via PBC regardless of periodic_molecules.
>
> Using freezegrps causes artifacts, especially with pressure coupling, so
> if you want to model the tubes as rigid, then the only real option that I
> can think of is to simply increase the force constant for the restraints.
>  I don't particularly understand this approach, as people have done tons of
> simulations of nanotubes with normal bonded geometry.
>
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
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