[gmx-users] Simulation of Glass Surfaces?

[AJ Lanphere]

Additionally, what is the difference between the different wall types? They
are stated as 9-3, 10-4, and 12-6, but I don't know what is meant by that.


On Tue, Aug 5, 2014 at 1:20 PM, AJ Lanphere <ajlanphere at gmail.com> 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.
> - 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.
>
> Thanks,
> AJ L
>
>
> On Mon, Jul 21, 2014 at 2:35 PM, David van der Spoel <spoel at xray.bmc.uu.se
> > wrote:
>
>> 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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>
>