DOI: 10.1063/1.458034. A second-order algorithm for the simulation of the Brownian dynamics of macromolecular models

A second-order algorithm for the simulation of the Brownian dynamics of macromolecular models

10.1063/1.458034

Crossref journal-article

AIP Publishing

The Journal of Chemical Physics (317)

Abstract

Most recent works on Brownian dynamics simulation employ a first-order algorithm developed by Ermak and McCammon [J. Chem. Phys. 69, 1352 (1978)]. In this work we propose the use of a second-order algorithm in which the step is a combination of two first-order steps, like in the second-order Runge–Kutta method for differential equations. Although the computer time per step is roughly doubled, the second-order algorithm is more efficient than the previous one because a given accuracy in the results can be achieved with less than half the number of steps. The new algorithm also allows for longer time steps without divergence. The advantage of the new procedure is illustrated in the simulation of four macromolecular systems: A quasirigid dumbbell, a semiflexible trumbbell, a semiflexible hinged rod, and a Gaussian polymer chain.

Bibliography

Iniesta, A., & GarcÃa de la Torre, J. (1990). A second-order algorithm for the simulation of the Brownian dynamics of macromolecular models. The Journal of Chemical Physics, 92(3), 2015â2018.

Authors 2

A. Iniesta (first)
J. García de la Torre (additional)

References 21 Referenced 115

10.1063/1.436761 / J. Chem. Phys. (1978)
10.1002/bip.360230113 / Biopolymers (1984)
10.1063/1.447563 / J. Chem. Phys. (1984)
10.1063/1.453526 / J. Chem. Phys. (1987)
10.1002/bip.360230214 / Biopolymers (1984)
10.1021/ma00155a019 / Macromolecules (1986)
10.1063/1.454283 / J. Chem. Phys. (1988)
10.1021/ma00181a045 / Macromolecules (1988)
10.1016/0032-3861(89)90115-8 / Polymer (1989)
10.1063/1.456046 / J. Chem. Phys. (1989)
10.1002/j.1538-7305.1979.tb02967.x / Bell System Tech. J. (1979)
10.1021/ma00158a042 / Macromolecules (1986)
10.1063/1.1681321 / J. Chem. Phys. (1974)
{'key': '2024021009214647600_r14', 'volume': '81', 'year': '1984', 'journal-title': 'J. Chem. Phys.'} / J. Chem. Phys. (1984)
10.1063/1.1681770 / J. Chem. Phys. (1974)
10.1016/S0006-3495(88)82956-4 / Biophys. J. (1988)
10.1063/1.440595 / J. Chem. Phys. (1980)
10.1002/bip.360271107 / Biopolymers (1988)
{'key': '2024021009214647600_r19'}
10.1039/F29858100591 / J. Chem. Soc. Faraday Trans. 2 (1985)
10.1063/1.445659 / J. Chem. Phys. (1983)

Dates

Type	When
Created	23 years, 1 month ago (July 26, 2002, 9:21 a.m.)
Deposited	1 year, 6 months ago (Feb. 10, 2024, 6:06 a.m.)
Indexed	1 week, 1 day ago (Aug. 29, 2025, 5:54 a.m.)
Issued	35 years, 7 months ago (Feb. 1, 1990)
Published	35 years, 7 months ago (Feb. 1, 1990)
Published Print	35 years, 7 months ago (Feb. 1, 1990)

Funders 0

None

BibTeX

@article{Iniesta_1990, title={A second-order algorithm for the simulation of the Brownian dynamics of macromolecular models}, volume={92}, ISSN={1089-7690}, url={http://dx.doi.org/10.1063/1.458034}, DOI={10.1063/1.458034}, number={3}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Iniesta, A. and García de la Torre, J.}, year={1990}, month=feb, pages={2015–2018} }

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