Often, additional complications make it harder to track down problems when considering binding free energy calculations. Solvation free energies provide a basic starting point for considering a number of the key issues, and are used frequently here because of this and because of their simplicity. While free energy calculations may be done for many different situations, here we focus on best practices for binding and solvation free energy calculations. A large part of the following discussion will discuss exactly how to construct useful and efficient pathways connecting the end states. Methods which are in principle correct may not always be practical or useful. ![]() Some pathways may be more efficient than others (sometimes by many orders of magnitude). Only after free energy estimates have converged can the underlying parameters and physical assumptions really be tested.įree energy is a function of state, so there are many possible choices of pathway for a thermodynamic cycle connecting the same two endpoints. Without convergence, agreement with experiment may be due only to fortuitous cancellation of error. The goal is to obtain that free energy with as little statistical error as possible - and not necessarily to match experiment. Given this particular set of parameters and physical assumptionstarting point, there exists a single right answer for a free energy calculation.
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