Module 3 : Classical Molecular Dynamics
Chapter 27 : A Sample Molecular Dynamics Program
 

The size of the simulation system is so chosen such that the number density in the simulation box corresponds to the experimental density of the system. Argon is a liquid at 85 K with density 1.40 gm/cc. Corresponding to this density at this temperature, 64 argon atoms are to be kept in a volume of 3.03×103Å3. (See problem 1 at the end of this chapter. Convert the density from gm/cc to number of particles per Å3by converting grams into moles and multiplying by Avogadro number. Also use, 1 cc = 1024Å3)The simulation box is usually taken to be cubic, this makes the box size to be 14.4744 A.

In order to prepare an initial configuration for the system, one may start with a simple cube, in which the argon atoms are placed on to the lattice sites. Given these initial positions r(t = 0) to the atoms, we need to choose an appropriate time step, Δt.

The potential energy function for argon is a simple Lennard-Jones 12-6 potential,

 

 (27.1)
Figure 27.1: The Lennard-Jones potential defined by the two parameters, s (particle diameter) and e (well-depth). The deeper the well-depth e, the stronger is the interaction between the two particles.