Molecular Dynamics

The two words in the title literally means:

Molecular: of or relating to molecules

Dynamics: the pattern or history of growth, change, and development in any field

Thus Molecular Dynamics tells you about a pattern or history of growth, change and development of molecules in any environment.

It is a computational method which allows one to understand time dependent movement of atoms and molecules. These movements of molecules are predicted based on the Newton's law of motion. The resulting forces on these atoms and molecules and their potential energy are defined with the help of different molecular mechanics force fields.

The Force fields consists of defined parameters like bond length, bond angles, torsions, Vander Waal forces etc. These force fields are specific for the kind of molecules treated. Thus, the force fields vary in nature depending on the parameters included and the type of target molecules. So, it is always advisable to understand the limits of force field you are planning to employ for your system.

Molecular Dynamics has applications in almost all fields of Science. Under the domain of Chemistry/ Biology, it is mostly applied in Material Science and Biological systems

Since Molecular Dynamics is based on Newton's laws of motion, the movement of atoms or molecules treated by MD are recorded in terms of atomic positions, velocities and acceleration. With the help of statistical mechanics, the information obtained at atomic level like atomic position, velocity etc can be used to determine thermodynamic properties of interest at macroscopic level like pressure, energy etc.

The statistical mechanics provides a bridge in the form of non-trivial mathematical equations connecting the thermodynamic properties to the movement of atoms and molecules.

Molecular Dynamics method thus provides a way to deal with movement of atoms and molecules following equations of motion thereby allowing one to solve these complex mathematical equations and yielding thermodynamic properties. In doing so, it requires the base of an ergodic hypothesis which states that “ The statistical ensemble averages are equal to time averages of the system.