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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
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
The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations
Marrink, S. J., Risselada, H. J., Yefimov, S., Tieleman, D. P., & de Vries, A. H. (2007) · The Journal of Physical Chemistry B · doi:10.1021/jp071097f · Cited by 5,562
Self-citationSimulating microscopic hydrodynamic phenomena with dissipative particle dynamics
Hoogerbrugge, P. J., & Koelman, J. M. V. A. (1992) · Europhysics Letters (EPL) · doi:10.1209/0295-5075/19/3/001 · Cited by 3,811
Statistical Mechanics of Dissipative Particle Dynamics
Español, P., & Warren, P. (1995) · Europhysics Letters (EPL) · doi:10.1209/0295-5075/30/4/001 · Cited by 2,835
A Leap-frog Algorithm for Stochastic Dynamics
Van Gunsteren, W. F., & Berendsen, H. J. C. (1988) · Molecular Simulation · doi:10.1080/08927028808080941 · Cited by 1,469
Self-citationMesoscopic model for solvent dynamics
Malevanets, A., & Kapral, R. (1999) · The Journal of Chemical Physics · doi:10.1063/1.478857 · Cited by 1,027
Dynamic Simulations of Hard-Sphere Suspensions Under Steady Shear
Koelman, J. M. V. A., & Hoogerbrugge, P. J. (1993) · Europhysics Letters (EPL) · doi:10.1209/0295-5075/21/3/018 · Cited by 833
Algorithms for brownian dynamics
van Gunsteren, W. F., & Berendsen, H. J. C. (1982) · Molecular Physics · doi:10.1080/00268978200100491 · Cited by 547
Self-citationHarvey, S. C., Tan, R. K.-Z., & Cheatham, T. E. (1998) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(199805)19:7<726::aid-jcc4>3.0.co;2-s · Cited by 399
An alternative approach to dissipative particle dynamics
Lowe, C. P. (1999) · Europhysics Letters (EPL) · doi:10.1209/epl/i1999-00365-x · Cited by 307
How would you integrate the equations of motion in dissipative particle dynamics simulations?
Nikunen, P., Karttunen, M., & Vattulainen, I. (2003) · Computer Physics Communications · doi:10.1016/s0010-4655(03)00202-9 · Cited by 224
Simulating the Physical World: Hierarchical Modeling from Quantum Mechanics to Fluid Dynamics
Berendsen, H. J. C. (2007) · Cambridge University Press eBooks · doi:10.1017/cbo9780511815348 · Cited by 213
Self-citationStochastic dynamics for molecules with constraints: Brownian dynamics of n-alkanes
van Gunsteren, W. F., Berendsen, H. J. C., & Rullmann, J. A. C. (1981) · Molecular Physics · doi:10.1080/00268978100102291 · Cited by 205
Self-citationFluctuation formulas in molecular-dynamics simulations with the weak coupling heat bath
Morishita, T. (2000) · The Journal of Chemical Physics · doi:10.1063/1.1287333 · Cited by 205
How would you integrate the equations of motion in dissipative particle dynamics simulations?
Nikunen, P., Karttunen, M., & Vattulainen, I. (2003) · TU/e Research Portal · Cited by 186
Junghans, C., Praprotnik, M., & Kremer, K. (2007) · Soft Matter · doi:10.1039/b713568h · Cited by 151
A common, avoidable source of error in molecular dynamics integrators
Lippert, R. A., Bowers, K. J., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossváry, I., & Shaw, D. E. (2007) · The Journal of Chemical Physics · doi:10.1063/1.2431176 · Cited by 116
Brownian dynamics simulation of a chemical reaction in solution
Allen, M. P. (1980) · Molecular Physics · doi:10.1080/00268978000102141 · Cited by 115
Andersen's canonical-ensemble molecular dynamics for molecules with constraints
Ryckaert, J.-P., & Ciccotti, G. (1986) · Molecular Physics · doi:10.1080/00268978600101851 · Cited by 62
Cited by
QuantumATK: an integrated platform of electronic and atomic-scale modelling tools
Smidstrup, S., Markussen, T., Vancraeyveld, P., Wellendorff, J., Schneider, J., Gunst, T., Verstichel, B., Stradi, D., Khomyakov, P. A., Vej-Hansen, U. G., et al. (2020) · Journal of Physics: Condensed Matter · doi:10.1088/1361-648x/ab4007 · Cited by 1,920
CHARMM-GUI supports the Amber force fields
Lee, J., Hitzenberger, M., Rieger, M., Kern, N. R., Zacharias, M., & Im, W. (2020) · The Journal of Chemical Physics · doi:10.1063/5.0012280 · Cited by 428
Accurate calculation of the absolute free energy of binding for drug molecules
Aldeghi, M., Heifetz, A., Bodkin, M. J., Knapp, S., & Biggin, P. C. (2016) · Chemical Science · doi:10.1039/c5sc02678d · Cited by 347
Soteras Gutiérrez, I., Lin, F.-Y., Vanommeslaeghe, K., Lemkul, J. A., Armacost, K. A., Brooks, C. L., & MacKerell, A. D. (2016) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2016.06.034 · Cited by 283
Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simulations with Implicit Solvent
Arnarez, C., Uusitalo, J. J., Masman, M. F., Ingólfsson, H. I., de Jong, D. H., Melo, M. N., Periole, X., de Vries, A. H., & Marrink, S. J. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/ct500477k · Cited by 278
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
