DOI: 10.1063/1.2431176. A common, avoidable source of error in molecular dynamics integrators

A common, avoidable source of error in molecular dynamics integrators

10.1063/1.2431176

Crossref journal-article

AIP Publishing

The Journal of Chemical Physics (317)

Abstract

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.

Bibliography

Lippert, R. A., Bowers, K. J., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., & Shaw, D. E. (2007). A common, avoidable source of error in molecular dynamics integrators. The Journal of Chemical Physics, 126(4).

Authors 8

Ross A. Lippert (first)
Kevin J. Bowers (additional)
Ron O. Dror (additional)
Michael P. Eastwood (additional)
Brent A. Gregersen (additional)
John L. Klepeis (additional)
Istvan Kolossvary (additional)
David E. Shaw (additional)

References 15 Referenced 103

{'key': '2023073120060088100_c1', 'first-page': '98', 'volume': '159', 'year': '1967', 'journal-title': 'Part. Part. Syst. Charact.'} / Part. Part. Syst. Charact. (1967)
10.1063/1.442716 / J. Chem. Phys. (1982)
{'volume-title': 'Computer Simulation of Liquids', 'year': '1987', 'key': '2023073120060088100_c3'} / Computer Simulation of Liquids (1987)
{'key': '2023073120060088100_c4', 'first-page': '327', 'volume': '23', 'year': '1977', 'journal-title': 'J. Comput. Chem.'} / J. Comput. Chem. (1977)
10.1002/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V / J. Comput. Chem. (2001)
10.1002/jcc.540130805 / J. Comput. Chem. (1992)
10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H / J. Comput. Chem. (1997)
10.1016/0021-9991(83)90014-1 / J. Comput. Phys. (1983)
10.1002/jcc.20290 / J. Comput. Chem. (2005)
10.1002/jcc.20291 / J. Comput. Chem. (2005)
10.1002/jcc.20289 / J. Comput. Chem. (2005)
10.1002/jcc.540040211 / J. Comput. Chem. (1983)
{'year': '2006', 'key': '2023073120060088100_c13'} (2006)
10.1007/978-94-015-7658-1 / In Intermolecular Forces by Pullman (1981)
10.1063/1.470117 / J. Chem. Phys. (1995)

Dates

Type	When
Created	18 years, 7 months ago (Jan. 26, 2007, 6:05 p.m.)
Deposited	2 months, 4 weeks ago (May 27, 2025, 4:20 p.m.)
Indexed	5 days, 3 hours ago (Aug. 22, 2025, 12:47 a.m.)
Issued	18 years, 6 months ago (Jan. 28, 2007)
Published	18 years, 6 months ago (Jan. 28, 2007)
Published Online	18 years, 6 months ago (Jan. 29, 2007)
Published Print	18 years, 6 months ago (Jan. 28, 2007)

Funders 0

None

BibTeX

@article{Lippert_2007, title={A common, avoidable source of error in molecular dynamics integrators}, volume={126}, ISSN={1089-7690}, url={http://dx.doi.org/10.1063/1.2431176}, DOI={10.1063/1.2431176}, number={4}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Lippert, Ross A. and Bowers, Kevin J. and Dror, Ron O. and Eastwood, Michael P. and Gregersen, Brent A. and Klepeis, John L. and Kolossvary, Istvan and Shaw, David E.}, year={2007}, month=jan }

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