Free energy perturbation (FEP) is a method based on statistical mechanics that is used in computational chemistry for computing free energy differences from molecular dynamics or Metropolis Monte Carlo simulations.

The FEP method was introduced by Robert W. Zwanzig in 1954. According to the free-energy perturbation method, the free energy difference for going from state A to state B is obtained from the following equation, known as the Zwanzig equation:

${\displaystyle \Delta F(\mathbf {A} \rightarrow \mathbf {B} )=F_{\mathbf {B} }-F_{\mathbf {A} }=-k_{\mathrm {B} }T\ln \left\langle \exp \left(-{\frac {E_{\mathbf {B} }-E_{\mathbf {A} }}{k_{\mathrm {B} }T}}\right)\right\rangle _{\mathbf {A} }}$

where T is the temperature, k_B is Boltzmann's 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 ΔF 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 or PMF.

Free energy perturbation calculations only converge properly when the difference between the two states is small enough; therefore it is usually necessary to divide a perturbation into a series of smaller "windows", which are computed independently. Since there is no need for constant communication between the simulation for one window and the next, the process can be trivially parallelized by running each window on a different CPU, in what is known as an "embarrassingly parallel" setup.