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
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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