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

Justin Lemkul jalemkul at vt.edu
Thu Oct 10 15:56:46 CEST 2013

On 10/10/13 9:54 AM, Steven Neumann wrote:
> Thank you. I do not have any explicit solvent in my system. I included the
> solvent in nonbonded parameters so not even implicit.

Well, presumably you have other things in the system, otherwise you're 
simulating an inert tube of non-interacting atoms, which I doubt is useful for 
anything.  Basically what I'm trying to say is freezegrps is listed as a 
non-equilibrium option for a reason - it does not correspond to physical reality 
and can seriously perturb your system in bad ways.  It's really only useful for 
equilibrating problematic systems, and nothing else IMHO.



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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