where T is the temperature, k B is the Boltzmann constant, and the angular brackets denote an average over a simulation run for state A. In practice, one runs a normal simulation for state A, but each time a new configuration is accepted, the energy for state B is also computed. The difference between states A and B may be in the atom types involved, in which case the Δ F obtained is for "mutating" one molecule onto another, or it may be a difference of geometry, in which case one obtains a free-energy map along one or more reaction coordinates. This free-energy map is also known as a potential of mean force (PMF).