When examining a system computationally one may be interested in knowing how the free energy changes as a function of some inter- or intramolecular coordinate (such as the distance between two atoms or a torsional angle).
The free energy surface along the chosen coordinate is referred to as the potential of mean force (PMF).
[1] The PMF can be obtained in Monte Carlo or molecular dynamics simulations to examine how a system's energy changes as a function of some specific reaction coordinate parameter.
For example, it may examine how the system's energy changes as a function of the distance between two residues, or as a protein is pulled through a lipid bilayer.
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.
is the average work needed to bring the two particles from infinite separation to a distance
is usually applied in the Boltzmann inversion method as a first guess for the effective pair interaction potential that ought to reproduce the correct radial distribution function in a mesoscopic simulation.
[5] Lemkul et al. have used steered molecular dynamics simulations to calculate the potential of mean force to assess the stability of Alzheimer's amyloid protofibrils.
[6] Gosai et al. have also used umbrella sampling simulations to show that potential of mean force decreases between thrombin and its aptamer (a protein-ligand complex) under the effect of electrical fields.