Method of calculating the non-binding potential of the coarse-grained model, calculating device of the non-binding potential of the coarse-grained model, and the calculation of the non-binding potential of the coarse-grained model program

摘要

PROBLEM TO BE SOLVED: To provide such a highly reliable method for calculating non-bonded potential of a coarse graining model that it is possible to acquire a radial distribution function without depending on a sample point of a discrete value.SOLUTION: A provided calculation method includes: steps ST2 to 5 of calculating discrete data which is a base of a radial distribution function of a coarse graining model in an equilibrium state on the basis of molecular dynamics calculation of an atomic model, and acquiring a target radial distribution function G(r) by approximating the calculated discrete data; and steps ST6 to 12 of calculating discrete data which is the base of the radial distribution function of the coarse graining model in the equilibrium state on the basis of molecular dynamics of the coarse graining model, acquiring a radial distribution function g(r) by approximating the calculated discrete data, and repeating correction of non-bonded potential and coarse-graining molecular dynamics calculation in order to have a small evaluation function including the radial distribution function g(r) and the target radial distribution function G(r). The method acquires a smoothed radial distribution function by performing a convolution arithmetic operation on discrete data and a predetermined window function.