- Free energy perturbation
**Free energy perturbation**(FEP) theory is a method based onstatistical mechanics that is used incomputational chemistry for computing free energy differences frommolecular dynamics orMetropolis Monte Carlo simulations. The FEP method was introduced by R. W. Zwanzig in 1954. [*Zwanzig, R. W. J. Chem. Phys. 1954, 22, 1420-1426. doi|10.1063/1.1740409*] According to free-energy perturbation theory, the free energy difference for going from state**A**to state**B**is obtained from the following equation, known as the "Zwanzig equation"::$Delta\; G(A\; ightarrow\; B)\; =\; G\_B\; -\; G\_A\; =\; -k\_B\; T\; ln\; left\; langle\; exp\; left\; (\; -\; frac\{E\_B\; -\; E\_A\}\{k\_B\; T\}\; ight\; )\; ight\; angle\; \_A$

where "T" is the

temperature , "k_{B}" isBoltzmann's constant , and the triangular brackets denote an average over a simulation run for state**A**. In practice, oneruns a normal simulation for state**A**, but each time anew configuration is accepted, the energy for state**B**is also computed. The differencebetween states**A**and**B**may be in the atom types involved, in which case the ΔGobtained is for "mutating" one molecule onto another, or it may be a difference ofgeometry, in which case one obtains a free energy map along one or morereaction coordinate s. This free energy map is also known as a "potential of mean force" or PMF.Free energy perturbation calculations only converge properly when the differencebetween the two states is small enough; therefore it is usually necessary to divide aperturbation into a series of smaller “windows”, which are computed independently.Since there is no need for constant communication between the simulation for onewindow and the next, the process can be trivially parallelized by running each window ina different CPU, in what is known as an “embarrassingly parallel ” setup.FEP calculations have been used for studying host-guest binding energetics,

pKa predictions, solvent effects on reactions, and enzymatic reactions. For thestudy of reactions it is often necessary to involve a quantum-mechanical representation ofthe reaction center because themolecular mechanics force field s used for FEP simulations can't handlebreaking bonds. A hybrid method that has the advantages of both QM and MMcalculations is calledQM/MM .An alternative to free energy perturbation for computing potentials of mean force is

umbrella sampling .**ee also***

Thermodynamic integration **References**

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