[gmx-users] carbon nanotube - ifnite in length ?
s.neumann08 at gmail.com
Thu Oct 10 16:01:22 CEST 2013
Thanks a lot. I will use position restraints then with a strong force
constant, no bonds and place the edge atoms within half of distance between
them from the box edge. Is that correct?
On Thu, Oct 10, 2013 at 2:56 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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 <jalemkul at outerbanks.umaryland.edu> | (410)
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