In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is broken. This causes a problem in the evaluation of electrostatic interaction under periodic boundary condition. A standard remedy for the problem is to consider a hypothetical homogeneous background charge density to neutralize the total system. Here, we present a new expression for the evaluation of electrostatic interactions for the system including the background charge by fast multipole method (FMM). Further, an efficient scheme to evaluate solute-solvent interaction energy by FMM has been developed to reduce the computation of far-field part. We have calculated hydration free energy of ions, Mg$^{2+}$, Na$^{+}$, and Cl$^{-}$ dissolved in neutral solvent using the new expression. The calculated free energy showed a good agreement with the result using well-established particle mesh Ewald method, demonstrating the validity of the present expression in the framework of FMM. An advantage of the present scheme is in an efficient free energy calculation of a large-scale charged systems (particularly over million particles) based on highly parallel computations.
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