[gmx-users] Simulation of Glass Surfaces?

[AJ Lanphere]

Thank you for the information that does sound like it would do what I'm
looking for, but could you possibly elaborate on how to set that up? I
don't see either of those terms in the manual, either under the run
parameters section about walls or otherwise.

Thanks,
AJ


On Tue, Aug 5, 2014 at 2:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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