Equipartition Principle for Internal Coordinate Molecular Dynamics

Abstract

The <i>principle of equipartition of (kinetic) energy</i> for all-atom Cartesian molecular dynamics states that each momentum phase space coordinate on the average has <i>kT</i>/2 of kinetic energy in a canonical ensemble. This principle is used in molecular dynamics simulations to initialize velocities, and to calculate statistical properties such as entropy. Internal coordinate molecular dynamics (ICMD) models differ from Cartesian models in that the overall kinetic energy depends on the generalized coordinates and includes cross-terms. Due to this coupled structure, no such equipartition principle holds for ICMD models. In this paper, we introduce noncanonical <i>modal coordinates</i> to recover some of the structural simplicity of Cartesian models and develop a new equipartition principle for ICMD models. We derive low-order recursive computational algorithms for transforming between the modal and physical coordinates. The equipartition principle in modal coordinates provides a rigorous method for initializing velocities in ICMD simulations, thus replacing the <i>ad hoc</i> methods used until now. It also sets the basis for calculating conformational entropy using internal coordinates