[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

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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