Fields free energy calculations

The quality of the mean-field approximation can be tested in simulations of the same lattice model [13]. Ideally, direct free-energy calculations of the liquid and solid phases would allow us to locate the point where the two phases coexist. However, in the present studies we followed a less accurate, but simpler approach we observed the onset of freezing in a simulation where the system was slowly cooled. To diminish the effect of supercooling at the freezing point, we introduced a terraced substrate into the system to act as a crystallization seed [14]. We verified that this seed had little effect on the phase coexistence temperature. For details, see Sect. A.3. At freezing, we have... 

As discussed in the example from the work of Hodel et al. [3], one of the most efficient ways to improve the accuracy of free energy calculations with a given force field is to enhance the conformational sampling. Thus, it is important to assess the extent to which phase space is covered. 

From (9.27), we see that this approach will work nicely if the variance is always small Taylor s theorem with remainder tells us that the error of the first-derivative - mean-field - contribution is proportional to the second derivative evaluated at an intermediate A. That second derivative can be identified with the variance as in (9.27). If that variance is never large, then this approach should be particularly effective. For further discussion, see Chap. 4 on thermodynamic integration, and Chap. 6 on error analysis in free energy calculations. 

Shirts, M. Pitera, J. Swope, W. Pande, V., Extremely precise free energy calculations of amino acid chain analogs comparison of common molecular mechanical force fields for proteins, J. Chem. Phys. 2003,119, 5740-5761. 

The book consists of 14 chapters, in which we attempt to summarize the current state of the art in the field. We also offer a look into the future by including descriptions of several methods that hold great promise, but are not yet widely employed. The first six chapters form the core of the book. In Chap. 1, we define the context of the book by recounting briefly the history of free energy calculations and presenting the necessary statistical mechanics background material utilized in the subsequent chapters. 

The background theory that underlies the FEP method as well as the molecular mechanics force fields that relate molecular structure to energy are reviewed in section one of the book. Section two describes the use of free energy calculations for determining molecular properties of ligands, including solvation, as calculated using both implicit and explicit water... 

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