I am using a (1,1,1) gold electrode for electron transport experiments using Transiesta. I have never used it before. I am wondering if when I do the electrode run, do I build a system where it is the left and right electrodes connected to each other? or do I use the entire device (molecule AND electrodes) and just set a flag in the file?

(In response to andselisk's request for more information about Transiesta: it is a computational chemistry program that is a part of the Siesta Suite. It is used mainly for electron transport calculations.)