From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Sat May 12 2018 - 16:27:42 CDT
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<mailto: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