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

Justin Lemkul jalemkul at vt.edu
Thu Sep 26 15:59:47 CEST 2013

On 9/26/13 8:39 AM, Steven Neumann wrote:
> Dear Gmx Users,
> I have my carbon nanotube and I wish to make it infinite in lenght. Which
> mdp options whall be used? pbc = xy and z is the infinite dimension?
> another issue: Would you apply bonds between carbon atoms within the
> nanotube or constraints using LINCS? Which of them is less computationally
> expensive for the run?

Use "pbc = xyz" in conjunction with "periodic_molecules = yes" otherwise the 
topology gets messed up trying to form unreasonable bonds.  The 
periodic_molecules keyword in the .mdp allows for bonds to be maintained over PBC.

I remember a very old post somewhere in the archive that said one should not 
apply pressure coupling along the axis of the nanotube, due to some difficulties 
with maintaining the bonded geometry, but since I have never done CNT 
simulations, take the fact that I'm just repeating what I've heard for what it's 
worth :)

Constraints always come with the cost of communication, so I would imagine 
harmonic bonds are "less expensive."  I really don't see constraints as a 
limiting factor for performance, though.



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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