Large-scale molecular dynamics simulations are increasingly applied to the study of wetting dynamics. They have the advantage of being able not only to model the macroscopic world with reasonable accuracy, but also to reveal details at the microscopic level. Here we review the principles of modeling, using molecular dynamics, and comment on the specific methods used in our laboratory in comparison with others. By way of example, we explain how we extract physical parameters from simulations of partially wetting liquids on homogeneous substrates in a variety of geometries. We then show how the results have been applied to build our understanding of the underlying mechanisms.