PROBLEM TO BE SOLVED: To provide a method for calculating an interaction between a main calculation object molecule and a sub calculation object molecule by using coordinate data which allows a solvent molecule to be disposed at an appropriate position around the calculation object molecules.SOLUTION: An interaction calculation method uses coordinates to calculate an interaction between a main calculation object molecule and a sub calculation object molecule, the coordinates being obtained by setting a periodic boundary condition and performing molecular dynamics calculation for the main calculation object molecule, the sub calculation object molecule, and a solvent molecule. The interaction calculation method includes a process which, with respect to coordinates of one solvent molecule at each time point obtained by the molecular dynamics calculation, selects the coordinates of the one solvent molecule from plural coordinates of the one solvent molecule existing in a unit lattice stipulated by the periodic b
