The predictive capabilities of MD simulations rely primarily on their connection to statistical mechanics. That is, the probabilities of observing certain states in an MD-generated trajectory define the thermodynamics in accordance with partition functions. Therefore, the energy surface sampled during the simulation must rely on appropriate model physics. The force field itself is a component of this requirement, but so too is the set of algorithms employed to perform the simulation. These algorithms include treatment of nonbonded forces, thermostats and barostats, time steps, and use of constraints, among other features.