Molecular dynamics (Molecular Dynamics, MD) here refers to the simulation method based on Newtonian mechanics. Different from the first-principles method based on quantum mechanics, MD simulation is realized by constructing the force field and solving the energy function, thus ignoring the deeper consideration of electronic details in the simulation. A significant advantage of this method is that it can handle systems on a larger scale than the first-principles method under the same hardware conditions. Through the MD simulation, the researchers can obtain the atomic trajectory of the system and observe the micro-dynamics at the atomic level. This dynamic simulation enables us to understand the motion and function of biological macromolecules, the interaction mechanism between proteins and small molecules, and the molecular self-assembly process of nanomaterials at the molecular level. As an important supplement to experimental methods, molecular dynamics simulation has been widely used in many fields, such as physics, chemistry, biomedicine, material science and so on.
