From: jashnvareh 1395 (jashnvareh1395_at_gmail.com)
Date: Sun May 13 2018 - 02:13:13 CDT
Thanks a lot for your prompt answers,
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,
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
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