“Checker Board” Periodic Boundary Conditions in Molecular Dynamics Codes

Abstract

Checker board periodic boundary conditions for molecular simulation are proposed. They represent a simple geometric transformation of the well known periodic boundary conditions formulae for variety of periodic and regular computational boxes (e.g. the truncated octahedron, rhombic dodecahedron, hexagonal prism, etc.) into a shifted parallelepiped periodic grid. As a result, the choice of an optional computational box shape is equivalent to the proper choice of the basic parallelepiped sides lengths.

The checker board periodic boundary conditions have been applied in a molecular dynamics (MD) code based on the link-cell method (using Lennard-Jones interactions). Simulation efficiency is approximately the same as for the classical cubic periodic boundary transformations.

Key Words:

• Molecular dynamics
• periodic boundary conditions
• Lennard-Jones potentials
• link-cell method
• computational algorithms