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

Justin Lemkul jalemkul at vt.edu
Thu Oct 10 15:37:47 CEST 2013

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 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 | (410) 706-7441


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