[gmx-users] Simulation of Glass Surfaces?

[Justin Lemkul]

On 8/5/14, 11:20 AM, AJ Lanphere wrote:
> So, I've been looking over the sections on walls in the manual and I have a
> few questions on the specifics.
> - Do the walls have to be composed of a solid material, or can they be set
> as just a boundary? I don't want my glass drifting out of the simulation
> box and into space, but I don't want it interacting with an interface,
> either.

Probably a flat-bottom potential (reflective boundary) is more along the lines 
of what you want.

> - Is it possible to remove periodicity from positive Z, but not negative Z?
> As in, can I set it up so that I'm only forming an "exposed" surface on one
> face of my box, instead of creating effectively a sheet of glass? I'm
> concerned that, since my simulation box is only 4.5nm on a side, creating
> two surfaces that close together will result in unrealistic structure.
>

AFAIK, no, you can't manipulate periodicity in this way.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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