It is not clear to me, how this “twist” can be realized properly.
Have you tried running your system without the interlayer potential added?
Does it maintain the expected structure?
When I visualize your data file, I see two small graphene leaflets in a huge box. When I look at the graphene sheet and interlayer potential examples, I see graphene sheets with proper periodic continuation across boundaries. Without that periodicity, the sheets will likely deform and crumble or do a variety of other strange changes, once you add some kinetic energy.
But then again, with periodic boundaries, it is not possible to have an arbitrary in plane rotation of one sheet against the other. Only selected angles are possible and which ones are possible depends on the system size as the rotated system also needs to have perfect periodic continuation.