Re: Creating an infinite graphene sheet

From: jashnvareh 1395 (jashnvareh1395_at_gmail.com)
Date: Sun May 13 2018 - 02:11:07 CDT

Thanks a lot for your prompt answers,

Hi Giacomo,

My question is that in the "topo addbond" command which atom id should be
selected for the periodic image?
I have the atom id of my real sheet at the edges but how about the atom id
for the periodic image?!

All the Best,
Zeynab

با احترام
دکتر زینب محمد حسینی
مدیریت آموزشی و پژوهشی مرکز آموزش عالی کاشمر

On Sun, May 13, 2018 at 1:57 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Yes. This how we do things like make infinite cellulose, although we have
> the benefit of specific patches to make the chemistry we are interested in.
> The most annoying part is making sure that you don't inadvertently
> introduce a defect at the boundary of the periodic cell. For graphene, this
> means making sure that your original sheet matches nicely at the edges.
>
> -Josh
>
>
>
> On 2018-05-12 12:25:04-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
>
> Hi, you could try using TopoTools to add bonds between atoms at the edges
> of the sheet. You could select them automatically, or using spatial
> criteria. To find the nearest neighbor of each edge atom, a selection
> based on "pbwithin" should help.
>
> Giacomo
>
> On Sat, May 12, 2018 at 11:34 AM, jashnvareh 1395 <
> jashnvareh1395_at_gmail.com> wrote:
>>
>> Dear all,
>> I want to run the simulation of an infinite graphene sheet solvated in
>> water.
>> I don't know how to create an infinite sheet with it's periodic images.
>> Should I add bonds between graphene and it's periodic images or is not
>> needed?
>> I searched within the forum but couldn't find a clear answer.
>> Would be so much thankful to help me..
>> All the Best,
>> Zeynab
>>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
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