Re: Creating an infinite graphene sheet

From: jashnvareh 1395 (
Date: Sun May 13 2018 - 02:27:42 CDT

Thanks a lot for your prompt answers,

Hi Giacomo,

My question is that in the "topo addbond" command which atom IDs should be
selected for the periodic image?
I want to create bond between an atom located at the boundary of the sheet
and the closest atom located at the boundary of the it's periodic image.
Which atom ID i have to consider for the periodic image as I only have the
ID for the real system and not for the periodic image?

All the Best,

On Sat, May 12, 2018 at 10:49 PM, Giacomo Fiorin <>

> 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 <
>> 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

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