Dear all,
I want to run the molecular dynamics simulation of an infinite graphene sheet solvated in water using NAMD code. 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?
Would be so much thankful to help me..
All the Best,
Zeynab
If you run your simulation box in a periodic boundary condition, you system will sense the infinite virtual boxes in xyz directions. But it is important how you use the simulator to construct your box-be careful about the bonds in the boundaries. Maybe you do not want to extend the sheets in three directions.
The study below can be helpful on how to prepare your simulation box.
Article Silver−Sodium Ion Exchange Dynamics in LTA Zeolite Membranes
yes it's impossible. I'm talking about infinity in term of periodic boundary condition (PBC) usually employed in Molecular Dynamics simulations.. It's just a common name used among simulators..
Graphene requires covalent bonds, which are not easy to cut by boundaries in classical mechanics terms (Force Field based approaches). Therefore, I think the setup you want to use is probably not feasible... or at least not easy at all to do rigurously. You might want to use a large supercell with a big graphene sheet and a droplet of water instead, or something along these lines.
If you really need to treat graphene as an infinite endless surface, I'd say you really need to jump to the QM realm. There, obviously, the treatment of solvents becomes the hard (and expensive) part.
hi Zeynab,
infinite graphene sheet solvated in water means that you want to have water on top and below your graphene sheet?
anyway, in any case if you want your graphene to be "infinite" using the PBC you definitely need to add the bonds going "through the box" to your FF
cheers
Hi Claire, that's exactly as you said. Thanks a lot..
Here is the NAMD mailing list where Josh answered me exactly how to do that along with all details :
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2017-2018/1856.html
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