text: The PMF can be obtained in Monte Carlo or molecular dynamics simulations to examine how a systems energy changes as a function of some specific reaction coordinate parameter. For example, it may examine how the systems energy changes as a function of the distance between two residues, or as a protein is pulled through a lipid bilayer. It can be a geometrical coordinate or a more general energetic (solvent) coordinate. Often PMF simulations are used in conjunction with umbrella sampling, because typically the PMF simulation will fail to adequately sample the system space as it proceeds.