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.
On Sun, May 13, 2018 at 3:11 AM, jashnvareh 1395 <jashnvareh1395_at_gmail.com>
> 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,
> 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>
>> 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.
>> 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.
>> 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
>>> 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
>>> I searched within the forum but couldn't find a clear answer.
>>> Would be so much thankful to help me..
>>> All the Best,
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
-- 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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