Module 3 : Classical Molecular Dynamics
Chapter 26 : Molecular Dynamics Simulations
 
 26.1. Introduction
With the advent of the computers, chemists, physicists and material scientists had begun(since 1950s) to exploit the power of the computers for probing the properties of materials through simulations. Almost all the materials of the physical world can be probed for their properties by designing appropriate simulation algorithms. These include atomic and molecular systems, biomolecules, complex materials, nuclear materials, life processes and the like
One can construct simulation schemes for the dynamics of the molecules present in the materials; i.e., the Molecular Dynamics (MD), where the constituents of the system are allowed to interact according to known laws of physics, over a period of time. Through the numerical solutions of the equations of motion (often described by the laws of Newtonian mechanics), one obtains the trajectories (position coordinates and/or velocities) of all the constituents of the system, under the influence of the interacting potential.

These trajectories are then analyzed in order to extract the desired properties such as pressure, stress, diffusion, viscosity, surface tension, dielectric constant, order parameter, autocorrelation functions, fluctuations, conformational changes etc. Since molecular systems generally consist of a vast number of particles, it is impossible to find the properties of such complex systems analytically. The MD simulation exercises circumvent this problem by using the numerical solutions of the equations of motion. Thus the MD simulation technique presents an interface between laboratory experiments and the theory. This often leads to the realization that ‘computer simulations’ are actually ‘computer experiments’.