[gmx-users] Simulation of Glass Surfaces?

AJ Lanphere ajlanphere at gmail.com
Tue Aug 5 19:21:19 CEST 2014

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,
- 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.


On Mon, Jul 21, 2014 at 2:35 PM, David van der Spoel <spoel at xray.bmc.uu.se>

> On 2014-07-21 18:33, AJ Lanphere wrote:
>> Hello all,
>> I am using GROMACS to simulate the melting and annealing of glasses.
>> Currently I've been working only with simulations of the glass bulk, with
>> periodic boundaries so the glass is connected on all sides. I was
>> wondering
>> if GROMACS can be used to simulate solid surfaces, because I have not seen
>> any methods for doing so in the manual and a brief literature search has
>> also not returned any useful references.
>>  We have done some stuff with glass surfaces:
> David van der Spoel, Erik J. W. Wensink and Alex C. Hoffmann: Lifting a
> glass from a wet table: a microscopic picture Langmuir 22 pp. 5666-5672
> (2006)
> you can also use analytic walls, check the manual.
>  Any advice would be greatly appreciated.
>> Regards,
>> AJ Lanphere
>> Graduate Student Researcher
>> Inamori School of Engineering, Alfred University
>> 1 Saxon Drive, Alfred, NY 14802
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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