The DOI matches its Crossref record; 28 of the 28 references it cites were found in a registry or an index.
Efficient Algorithms for Langevin and DPD Dynamics
Open accessAbstract
In this article, we present several algorithms for stochastic dynamics, including Langevin dynamics and different variants of Dissipative Particle Dynamics (DPD), applicable to systems with or without constraints. The algorithms are based on the impulsive application of friction and noise, thus avoiding the computational complexity of algorithms that apply continuous friction and noise. Simulation results on thermostat strength and diffusion properties for ideal gas, coarse-grained (MARTINI) water, and constrained atomic (SPC/E) water systems are discussed. We show that the measured thermal relaxation rates agree well with theoretical predictions. The influence of various parameters on the diffusion coefficient is discussed.
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Molecular dynamics with coupling to an external bath
Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984) · The Journal of Chemical Physics · doi:10.1063/1.448118 · Cited by 30,700
Self-citationCanonical dynamics: Equilibrium phase-space distributions
Hoover, W. G. (1985) · Physical Review A · doi:10.1103/physreva.31.1695 · Cited by 23,465
Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. C. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90098-5 · Cited by 21,239
Self-citationLINCS: A linear constraint solver for molecular simulations
Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(199709)18:12<1463::aid-jcc4>3.0.co;2-h · Cited by 18,260
Self-citationCanonical sampling through velocity rescaling
Bussi, G., Donadio, D., & Parrinello, M. (2007) · The Journal of Chemical Physics · doi:10.1063/1.2408420 · Cited by 18,089
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008) · Journal of Chemical Theory and Computation · doi:10.1021/ct700301q · Cited by 15,908
The missing term in effective pair potentials
Berendsen, H. J. C., Grigera, J. R., & Straatsma, T. P. (1987) · The Journal of Physical Chemistry · doi:10.1021/j100308a038 · Cited by 13,345
Self-citationSettle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
Miyamoto, S., & Kollman, P. A. (1992) · Journal of Computational Chemistry · doi:10.1002/jcc.540130805 · Cited by 7,344
Nosé–Hoover chains: The canonical ensemble via continuous dynamics
Martyna, G. J., Klein, M. L., & Tuckerman, M. (1992) · The Journal of Chemical Physics · doi:10.1063/1.463940 · Cited by 5,924
Molecular dynamics simulations at constant pressure and/or temperature
Andersen, H. C. (1980) · The Journal of Chemical Physics · doi:10.1063/1.439486 · Cited by 5,758
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Self-citation
Metadata
- Authors
- Goga, N., Rzepiela, A. J., de Vries, A. H., Marrink, S. J., & Berendsen, H. J. C.
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-06-13
- Volume
- 8
- Issue
- 10
- Pages
- 3637-3649
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- OpenAlex
- W2320513108
- Cited by
- 334
- References
- 28
- FWCI
- 4.77
- Type
- journal article
- Language
- en
- Open access
- hybrid
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