Programming of a simple molecular dynamic simulation using open source software

Abstract

Molecular Dynamics (MD) simulation is a technique for computing equilibrium and dynamic properties of a classical many-body system. The key ingredients in carrying out a MD simulation are the potentials used to model intermolecular interactions, the integration algorithms and the periodic boundary conditions (PBC) to conserve the total energy of the system.Researchers generally use expensive software packages to run model simulations and therefore, face many limitations when further improvements and expansions are required. Open source software provides much more freedom and more expansion capabilities in programming. Thus, in this research project a simple MD simulation model was developed using java 6.0 programming language and equilibrium of a real gas under Lennard-Jones(LJ) potential with periodic boundary conditions was studied using the simulation programme.