Joshua T. Berryman, Tanja Schilling
Sets of free energy differences are useful for finding the equilibria of chemical reactions, while absolute free energies have little physical meaning, however finding the relative free energy by subtraction of absolute free energies is a valuable strategy in certain important cases. We present calculations of absolute free energies of biomolecules, using a combination of the well-known Einstein Molecule method (for treating the solute) with a conceptually related liquid method of recent genesis (for treating the solvent and counterions). The approach is based on thermodynamic integration from a detailed atomistic model to one which is simplified but analytically solvable, thereby giving the absolute free energy as that of the tractable model plus a correction term found numerically. An example calculation giving the free energy with respect to salt concentration for the B- and Z-isomers of duplex DNA in explicit solvent and counterions is presented.
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http://arxiv.org/abs/1207.5455
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