We are doing molecular dynamics to understand behavior of atoms and molecules in a microscopic (nanoscopic!) scale. Since we generally only need one force field (say, a simple simulation) we can extract a lot of useful data like, for example, diffusion kinetics, adsorption dynamics, permeability, phase equilibrium (this last better with MC?).

Fixing temperature and/or pressure is done to simulate an experimental system, where isothermal or constant pressure conditions are commonly encountered.

Hi Smruti,

We do MD simulations because we can and because there are certain things that we can not study experimentally yet (eg, quantum mechanics studies) or to add some additional explanations to an experimental observable, like protein-ligand interaction, conformational changes, etc, etc