Thanks for your reply, Anders.
I have read your paper: doi:10.1103/PhysRevB.85.165442 .
I think the configuration I would like simulate is very similar to the nickel-graphene case (just need to replace the nickel atoms with doped-silicon, and add a vertical gate bias on the interface of nickel and graphene).
If you still do not understand what the configuration is, please have a look at this paper:
[ J. Chauhan, A. Rinzler, and J. Guo, "A Computational Study of Graphene Silicon Contact", J. Appl. Phys., vol. 112, p. 104502, 2012. ]
Download address:
http://scitation.aip.org/content/aip/journal/jap/112/10/10.1063/1.4759152The gated graphene-doped_silicon contact presented in it is exactly what I would like to study with ATK.
I hope all your confusions should be clear in it and I am looking forward to your suggestions.
Best