This project is to study the new methods of molecular dynamics simulations for ligand and receptor interaction, establish reasonable optimization models, develop efficient numerical algorithms by using evolutionary algorithms, response surface methodology together with traditional optimization methods. By introducing the dual mixed variables the symplectic algorithms of molecular dynamics will be proposed and developed them to the asynchronous parallel systematic methodology. To be oriented with engineering applications, the above-mentioned developments will be finally integrated to produce applied software for biochemistry analysis and drug design, which can simulate the interaction and motion among the molecule in a large system speedily and efficiently.