Molecular Dynamics Method
Molecular Dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules. In this computational method, atoms/molecules are allowed to interact for a fixed period of time, giving a view of the dynamic evolution of the system. Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such complex systems analytically. MD simulation circumvents this problem by using numerical approaches. However, long MD simulations are mathematically ill-conditioned, generating cumulative errors in numerical integration that can be minimized with proper selection of algorithms and parameters. In the most common version of MD packages, the trajectories of atoms and molecules are determined by numerically solving Newton’s equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanics force-fields. This method was originally developed within the field of theoretical physics in the late 1950s but is applied today mostly in chemical physics, materials science and the modelling of biomolecules. In other words, MD method was first introduced by Alder and Wainwright in the late 1950’s to study the interactions of hard spheres. Technically, many important insights concerning the behavior of simple liquids emerged from their studies.
Historically, next major advance was in 1964, when Rahman carried out the first simulation using a realistic potential for liquid argon. Also, the first MD simulation of a realistic system was done by Rahman and Stillinger in their simulation of liquid water in 1974. Later, the first protein simulations appeared in 1977 with the simulation of the bovine pancreatic trypsin inhibitor. MD approach is frequently used to refine 3-dimensional structures of proteins and other macromolecules based on experimental constraints from X-ray crystallography or NMR spectroscopy. Further, MD is used to examine the dynamics of atomic-level phenomenon that cannot be observed directly, such as thin film growth and ion-subplantation, and also to examine the physical properties of nanotechnological devices that have not or cannot yet be created. In biophysics and structural biology, this method is frequently applied to study the motions of macromolecules such as proteins and nucleic acids, which can be useful for interpreting the results of certain biophysical experiments and for modeling interactions with other molecules, as in ligand docking.
Reference
D. C. Rapaport (1996) The Art of Molecular Dynamics Simulation. ISBN 0-521-44561-2.