From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sun May 13 2018 - 10:53:39 CDT
Obviously for each atom you should exclude the atom itself from the
selection. Also, you should set the periodic boundary conditions correctly
for VMD. Why don't you experiment first with a linear polymer, and do the
more time-consuming 2D graphene sheet later?
On Sun, May 13, 2018 at 11:34 AM, jashnvareh 1395 <jashnvareh1395_at_gmail.com>
wrote:
> 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.
>>>>> 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
>>
>
>
-- 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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