From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sun May 13 2018 - 10:08:46 CDT
For the edge of the nearest periodic image, I suggested you to use an atom
selection based on "pbwithin" for each of the edge atoms.
Giacomo
On Sun, May 13, 2018 at 3:11 AM, jashnvareh 1395 <jashnvareh1395_at_gmail.com>
wrote:
> 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
>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgoo.gl%2FQ3TBQU&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C9aeb02ac3f194ab68a6608d5b835ac36%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636617463035631609&sdata=y%2BjikkoGuqDMiQkZxpeGi5OtCckmgjmT2PbYEoZbLpk%3D&reserved=0>
>> https://github.com/giacomofiorin
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgiacomofiorin&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C9aeb02ac3f194ab68a6608d5b835ac36%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636617463035641614&sdata=jNz87wupVjyfyQmhBaqfv7OuRrEXXj3vGAUDOa4ZEPs%3D&reserved=0>
>>
>>
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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