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An alternative to free-energy perturbation for computing potentials of mean force in chemical space is thermodynamic integration. Another alternative, which is probably more efficient, is the Bennett acceptance ratio method. Adaptations to FEP exist which attempt to apportion free-energy changes to subsections of the chemical structure. [5]
Because the free energy of a system is not simply a function of the phase space coordinates of the system, but is instead a function of the Boltzmann-weighted integral over phase space (i.e. partition function), the free energy difference between two states cannot be calculated directly from the potential energy of just two coordinate sets (for ...
This method, also called Free energy perturbation (or FEP), involves sampling from state A only. It requires that all the high probability configurations of super state B are contained in high probability configurations of super state A, which is a much more stringent requirement than the overlap condition stated above.
Therefore, only relative free energy values, or changes in free energy, are physically meaningful. The free energy is the portion of any first-law energy that is available to perform thermodynamic work at constant temperature, i.e., work mediated by thermal energy. Free energy is subject to irreversible loss in the course of such work. [1]
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). If the system of ...
where () is the free-energy profile of the unbiased system, and () is the free-energy profile calculated for the biased, umbrella-sampled system. Series of umbrella sampling simulations can be analyzed using the weighted histogram analysis method (WHAM) [2] or its generalization. [3]
The energy is replaced by the characteristic potential of that ensemble, the Gibbs Free Energy. The letter Z stands for the German word Zustandssumme , "sum over states". The usefulness of the partition function stems from the fact that the macroscopic thermodynamic quantities of a system can be related to its microscopic details through the ...
Free-energy relationship, a relationship in physical organic chemistry; Principle of minimum energy, a thermodynamic formulation based on the second law; Thermodynamic free energy, the energy in a physical system that can be converted to do work, including: Gibbs free energy; Landau free energy (also known as grand potential) Helmholtz free energy