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

[Steven Neumann]

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...

Steven


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
>
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> Justin A. Lemkul, Ph.D.
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