Thermodiffusion can be simulated in various ways by molecular simulations, where non-equilibrium molecular dynamics (NEMD) simulations are a well-established standard approach. These simulations closely mimic experimental scenarios for thermodiffusion measurements, making them the ideal candidates to construct benchmark data. NEMD simulations monitor the response to system perturbations out of equilibrium. Synthetic NEMD simulations add external forces on molecules, thus altering their dynamics in an artificial way. On the contrary, boundary-driven NEMD methods aim at paralleling experimental situations much more directly by their conceptual set-up. These methods impose different temperatures within the simulation volume that give rise to temperature gradients, which, in turn, exert thermodynamic forces on the molecules in an indirect and natural way. Typically, a narrow region along one spatial direction is assigned as a heat source volume, and a corresponding heat sink region is placed half the simulation volume apart. The difference between the various boundary-driven methods is the way in which the temperature is controlled in the two regions.