The application of molecular dynamic simulations

Abstract

Molecular dynamic(MD) simulations have been developed into a mature tool for researchers and have had a huge impact on the aspects of drug discovery, molecular biology, and prediction of specific structures and related functions of macromolecules in recent years. The aim of this article is to provide some essential knowledge about the theories and applications of this useful technology. This introduction to molecular dynamics starts from the definition of some basic concepts, including the molecular mechanics force fields and how they are applied to the motion systems of molecular dynamics simulations and their developments recently. Also, the outstanding strengths and limitations of the MD simulations are discussed, as are some possible solutions to them. This article shows the wide applications of MD simulations, including drug discovery, prediction of structure, and allostery. Due to the growing power of computational calculations and its important role in simulating the biological process between receptors and ligands like allosteric binding sites, MD simulations are thought to be more and more important in the near future.