Abstract:

The role of molecular dynamics simulation in the research of chemistry and related disciplines has become increasingly prominent. However, it is rarely involved in undergraduate chemistry experiments. Existing computational chemistry experiments mostly focus on the calculation of molecular properties by quantum chemistry methods. To popularize molecular dynamics simulation as a powerful tool in undergraduate experimental teaching and help students understand the dynamic behavior of molecules, alanine dipeptide is used as an example to design a simple molecular dynamics simulation experiment. Through this experiment, students can grasp the basic principles, processes, and result processing methods of molecular dynamics simulation. Furthermore, it can deepen their understanding of abstract concepts, such as potential energy surfaces, in physical chemistry. This experiment can be used as the content of a computational chemistry experiment or as an extended physical chemistry experiment.

Key words: Molecular simulation, Computational chemistry, Molecular dynamics, Physical chemistry experiment