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Journal of Chemical Physics / Volume 126 / Issue 4 / LETTERS TO THE EDITOR / Notes
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J. Chem. Phys. 126, 046101 (2007); http://dx.doi.org/10.1063/1.2431176 (2 pages)

A common, avoidable source of error in molecular dynamics integrators

Ross A. Lippert1, Kevin J. Bowers1, Ron O. Dror1, Michael P. Eastwood1, Brent A. Gregersen1, John L. Klepeis1, Istvan Kolossvary1, and David E. Shaw2

1D. E. Shaw Research, LLC, New York, New York 10036
2D. E. Shaw Research, LLC, New York, New York 10036 and Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032

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(Received 24 October 2006; accepted 11 December 2006; published online 29 January 2007)

In constrained molecular dynamics simulations using some of the most popular molecular dynamics codes, calculation of the velocities of constrained particles is based solely on the differences in particle positions during two successive time steps. This creates a numerical instability that the authors’ show to be signicant in a typical single-precision floating-point simulation. They describe a simple modification that eliminates this source of instability and demonstrate that this change substantially reduces the energy drift of a sample single-precision NVE simulation.

© 2007 American Institute of Physics

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KEYWORDS and PACS

Keywords

molecular dynamics method, water

PACS

  • 61.20.Ja

    Computer simulation of liquid structure

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.2431176

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

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  16. The result is similar if deltat is not such a power, with extra roundoff terms from the arithmetic.

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Figures (1) Tables (1)

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FIG.1
Energy drift for our test simulations using SPC water (Ref. 14), smooth particle mesh Ewald (Ref. 15) with fourth order B splines, 1/β = 2.96 Å, a 1 Å mesh spacing, 10 Å van der Waals and 12 Å Coulomb cutoffs, and neighbor list updates every time step (δt = 1 fs).

FIG.1 Download High Resolution Image (.zip file) | Export Figure to PowerPoint

Tables

Table I. Common integration methods: parentheses indicate the customary computational ordering (Ref. 3).

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