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 systematically change the proportion of total kinetic energy (KE) found in motions associated with the various degrees of freedom. Under these conditions, the simulation...
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Published in | Journal of computational chemistry Vol. 19; no. 7; pp. 726 - 740 |
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Main Authors | , , |
Format | Journal Article |
Language | English |
Published |
New York
John Wiley & Sons, Inc
01.05.1998
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Subjects | |
Online Access | Get full text |
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Summary: | This article describes an unexpected phenomenon encountered during MD simulations: velocity rescaling using standard protocols can systematically change the proportion of total kinetic energy (KE) found in motions associated with the various degrees of freedom. Under these conditions, the simulation violates the principle of equipartition of energy, which requires a mean kinetic energy of RT/2 in each degree of freedom. A particularly pathological form of this problem occurs if one does not periodically remove the net translation of (and 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 almost no kinetic energy associated with the internal degrees of freedom. We call this phenomenon “the flying ice cube.” We present a mathematical 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 diatomic system, one involving a low resolution model of DNA in vacuo, and the third using a traditional all‐atom DNA model with full solvation, periodic boundary conditions, and the particle mesh Ewald method for treating long‐range electrostatics. Finally, we discuss methods for avoiding the problem. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 726–740, 1998 |
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Bibliography: | istex:A993DD7532DA3A09BF0511AC0CF9F159828E0ACD ark:/67375/WNG-XXSPTMMP-V ArticleID:JCC4 Pittsburgh Supercomputing Center - No. MCA935017P National Institutes of Health - No. HL-34343; No. CA-25644 |
ISSN: | 0192-8651 1096-987X |
DOI: | 10.1002/(SICI)1096-987X(199805)19:7<726::AID-JCC4>3.0.CO;2-S |