THE FLYING ICE CUBE - VELOCITY RESCALING IN MOLECULAR-DYNAMICS LEADS TO VIOLATION OF ENERGY EQUIPARTITION

This article describes an unexpected phenomenon encountered during MD simulations: velocity rescaling using standard protocols can systemati cally change the proportion of total kinetic energy (KE) found in moti ons associated with the various degrees of freedom. Under these condit ions, the simulation violates the principle of equipartition of energy , which requires a mean kinetic energy of RT/2 in each degree of freed om. A particularly pathological form of this problem occurs if one doe s not periodically remove the net translation of land rotation about) the center of mass. In this case, almost all of the kinetic energy is converted into these two kinds of motion, producing a system with almo st no kinetic energy associated with the internal degrees of freedom. We call this phenomenon ''the flying ice cube.'' We present a mathemat ical analysis of a simple diatomic system with two degrees of freedom, to document the origin of the problem. We then present examples from three kinds of MD simulations, one being an in vacuo simulation on a d iatomic system, one involving a low resolution model of DNA in vacuo, and the third using a traditional all-atom DNA model with full solvati on, periodic boundary conditions, and the particle mesh Ewald method f or treating long-range electrostatics. Finally, we discuss methods for avoiding the problem. (C) 1998 John Wiley & Sons, Inc.