From: jashnvareh 1395 (jashnvareh1395_at_gmail.com)
Date: Sun May 13 2018 - 10:34:11 CDT
Thanks a lot for the reply. Maybe I'm wrong but when I try for example
"pbwithin 3 of my edge selection" it gave me the indices within the same
sheet and not in it's periodic images. if I add bond for those atoms I get
a long bond from one edge to the opposite edge of the primary sheet..
May you guide me on that?
با احترام
دکتر زینب محمد حسینی
مدیریت آموزشی و پژوهشی مرکز آموزش عالی کاشمر
On Sun, May 13, 2018 at 7:38 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> 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--000000000000d9c017056c1819e3--
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