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

[Justin Lemkul]

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.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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