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A computational methodology to treat the covalent boundary between QM and MM regions in the Effective Fragment Potential (EFP) method, by defining a buffer region consisting of frozen localized molecular orbitals (LMOs), is introduced. The implementation of energy, gradient, and EFP parameter evaluations in the presence of frozen LMOs is discussed. The magnitude and source of errors introduced by various choices of buffer region is studied for the proton affinities of lysine and the tripeptide glycine-lysine-glycine. It is shown that by reasonable choice of the frozen density buffer region the proton affinity error can be consistently decreased to less than 0.5 kcal/mol compared to the full ab initio calculation.