Molecular dynamics (MD) simulations essentially consist of numerically integrating Hamilton's, Newton's or Lagrange's equations of motion using small integration time steps. Although these equations are valid for any set of conjugate positions and momenta, the use of Cartesian coordinates greatly simplifies the kinetic energy term. The resulting coupled first-order, ordinary differential equations can be solved using numerical integrators. Despite the simplicity of MD methods, the simulation of millions of atoms over long time scales like seconds is not possible without substantial reduction of the number of equations-of-motion, a feat typically achieved by course graining groups of atoms into one element. This approach not only reduces the number of equations, but if proper separation of the time scales for motion can be achieved, it also allows the use of considerably larger integration time steps and thus helps bridge the large gap between simulation and experimental time scales.