Introduction
The atoms in biomolecules are always in constant motion, and the functions of molecules and the interactions between them are closely related to the dynamics of the molecules involved. In other words, to understand the working mechanism of proteins or other biomolecules, molecular biologists must first be able to clearly know the movement patterns of these biomolecules, and can interfere with their motion at the atomic level to get the response of the biomolecules. Since it is difficult for molecular biologists to directly observe the motion of a single atom and perturb its motion in a desired way, molecular dynamics simulation has come into being. Molecular dynamics (MD) is a computer simulation technique that analyzes the physical movements of atoms and molecules by using a general model of the physics governing interatomic interactions. Through this technology, researchers can obtain the trajectory of the atoms in a fixed period of time, and can observe various microscopic details of this process, which makes it possible to predict the time evolution of a system of interacting particles, such as atoms, molecules, and granules. In order to complete a molecular dynamics simulation, experimenters need the definition of a potential function, and among them, two common and important potentials are empirical potentials and potentials in ab initio methods.
Empirical Potentials
The empirical potential energy function is a potential widely used in atomistic computer simulations, which is particularly common in molecular-dynamics and Monte-Carlo methods. In different disciplines, the empirical potential has different names. For example, it is called the force field in chemistry while it is named the interatomic potential in materials physics. The empirical potential in chemistry, that is, the force field, usually refers to the sum of bonded forces related to chemical bonds, bond angles, and bond dihedrals, and non-bonded forces connected with van der Waals forces and electrostatic charge. And the non-local nature of non-bonded interactions determines that these potentials contain at least the weak interactions among all particles during the motion. Generally speaking, the force field adopts numerical approximations, such as shifted cutoff radii and reaction field algorithms, so as to reduce the computational cost and increase the calculation speed of the molecular dynamics simulation.
Potentials in Ab Initio Methods
Ab initio quantum chemistry method is a computational chemistry method combined with quantum chemistry, which is first proposed and used by Robert Parr and his colleagues. “Ab initio,” translated as “from the beginning” or “from first principles,” means that only physical constants are put into the ab initio calculation method. By associating the ab initio calculation method with the molecular dynamics simulation, ab initio molecular dynamics (AIMD) emerges, which refers to the use of a quantum mechanical method and potentials to obtain electronic behaviors from the beginning so as to obtain more accurate chemical reactions. However, because of the high cost of dealing with electronic degrees of freedom, the simulation cost of this method is much higher than that of traditional molecular dynamics simulations. Therefore, the ab initio molecular dynamics simulation method is only used for simulation of smaller systems and shorter time.
Conclusion
The study of the macromolecules structure is a key to understanding biology as well as an important factor in promoting the development of other disciplines. However, because a molecular system is usually composed of a large number of particles, it is impossible for people to directly obtain the properties and functions of this complex system. After years of research and testing, molecular dynamics simulation, with numerical methods, has successfully provided researchers in various fields with an effective way to understand and analyze the structure and function of macromolecules. At present, this technology has matured and has been widely used in many fields, such as chemical physics, materials science, and biophysics, and it will continue to serve as an important means of scientific experiment and research in the future.
