Absolute Free Energies for Biomolecules in Implicit or Explicit Solvent

Abstract

Methods for absolute free energy calculation by alchemical transformation of a quantitative model to an analytically tractable one are discussed. These absolute free energy methods are placed in the context of other methods, and an attempt is made to describe the best practice for such calculations given the current state of the art. Calculations of the equilibria between the four free energy basins of the dialanine molecule and the two right-and left-twisted basins of DNA are discussed as examples.