I think you are confusing reducing dimensions with making dimensionless :P
With dimension reduction I mean: If you have an N-dimensional system (for example with states in \mathbb{R}^N ) then there could be symmetries present which allow you to move the system to an M-dimensional system with M < N. This is a useful trick in the study of Hamiltonian systems.
RE: A toy example of molecule aggregation to familiarize with LAMMPS software