I guess the best thing to do is try other alternatives (instead simulation packages) in order to simulate such low-dimensional systems. You could try to solve the Schrodinger equation numerically, using finite elements methods like Split Operator. When using methods like that, you will be able to be confident with all the parameters involved in the simulation. 

http://www.comsol.com/model/723 - only for single-particle calculation 

thanks for answering