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
--
==================================================
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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