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. Author manuscript; available in PMC: 2010 Aug 1.
Published in final edited form as: J Comput Chem. 2009 Aug;30(11):1680–1691. doi: 10.1002/jcc.21337

Figure 2.

Figure 2

Stages used in the free energy calculation of a four-fragment molecule, corresponding to Eq. (10). The initial stages proceed in analogy to Fig. 1, with pair-wise interactions added one at a time for neighboring (“bonded”) fragments. In the final stage, all remaining interactions are added. Other, more incremental staging schemes are possible, but were not necessary in the present study.