A higher version of an integrated molecular dynamics program, NEW-RYUDO with an extension for chemical reaction. Usually, molecular dynamics method cannot deal with chemical reaction, which inherently involves an electron transfer between atoms because the method is based on classical mechanics. This program stochastically deals with chemical reactions within a scheme of classical mechanics, thus realizing the study of chemical reaction dynamics of large complex systems. This program has been applied to the investigations of proton hopping with the consideration of Grotthus mechanism, polymerization reaction, and so on.