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The potential utility and limitations of two methods to determine free energy differences from molecular dynamics simulations (MD) are studied. The computation of the free energy of hydration of the inert gases serves as a simple but illustrative example. Good results are obtained for the inert gases from a perturbation treatment, using a reference ensemble obtained from a MD simulation of a cavity in water, if these atoms are comparable in size to the cavity and the calculated free energy differences are small. This limits the applicability of the perturbation treatment of a small number of cases. Larger free energy differences can be obtained with reasonable accuracy from MD simulations with continuously changing interaction parameters. This integration method is more generally applicable, but makes an additional simulation necessary.
Straatsma et al. (Mon,) studied this question.