Introducing MD theory
MD is based on simulating individual particle trajectories over a desired time period to analyze the time evolution of an entire system of particles in a solid, liquid, or gaseous state. Each particle (usually an atom) is allowed to traverse in space as determined by Newton's laws of classical dynamics, where the atomic positions, velocities, and accelerations at one point in time are used to calculate the corresponding kinematics quantities at a different point in time. This process is repeated over a sufficiently long-time interval for every atom in a system, and the final configuration of the atoms indicates the time evolution of the system over the said time interval.
Typical MD simulations are limited to the study of atomistic systems consisting of atoms in the range of 
to 
, occupying a simulation box with a length in the order of nanometers, over a regular timescale of nanoseconds. MD simulations of such microscopic systems are relevant when the systems are able to represent the time evolution of corresponding macroscopic systems.
The theory behind MD is described briefly in the following sections. For a more detailed understanding, you are advised to refer to the dedicated literature on MD theory (Computer Simulation of Liquids by Michael P. Allen and Dominic J. Tildesley, and Understanding Molecular Simulation by Daan Frenkel and Berend Smit).
