Publication

Benchmark of Schemes for Multiscale Molecular Dynamics Simulations

Goga, N., Melo, M. N., Rzepiela, A. J., de Vries, A., Hadar, A., Marrink, S. J. & Berendsen, H., Apr-2015, In : Journal of Chemical Theory and Computation. 11, 4, p. 1389-1398 10 p.

Research output: Contribution to journalArticleAcademicpeer-review

APA

Goga, N., Melo, M. N., Rzepiela, A. J., de Vries, A., Hadar, A., Marrink, S. J., & Berendsen, H. (2015). Benchmark of Schemes for Multiscale Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 11(4), 1389-1398. https://doi.org/10.1021/ct501102b

Author

Goga, N. ; Melo, M. N. ; Rzepiela, A. J. ; de Vries, Alex ; Hadar, A. ; Marrink, S. J. ; Berendsen, Herman. / Benchmark of Schemes for Multiscale Molecular Dynamics Simulations. In: Journal of Chemical Theory and Computation. 2015 ; Vol. 11, No. 4. pp. 1389-1398.

Harvard

Goga, N, Melo, MN, Rzepiela, AJ, de Vries, A, Hadar, A, Marrink, SJ & Berendsen, H 2015, 'Benchmark of Schemes for Multiscale Molecular Dynamics Simulations', Journal of Chemical Theory and Computation, vol. 11, no. 4, pp. 1389-1398. https://doi.org/10.1021/ct501102b

Standard

Benchmark of Schemes for Multiscale Molecular Dynamics Simulations. / Goga, N.; Melo, M. N.; Rzepiela, A. J.; de Vries, Alex; Hadar, A.; Marrink, S. J.; Berendsen, Herman.

In: Journal of Chemical Theory and Computation, Vol. 11, No. 4, 04.2015, p. 1389-1398.

Research output: Contribution to journalArticleAcademicpeer-review

Vancouver

Goga N, Melo MN, Rzepiela AJ, de Vries A, Hadar A, Marrink SJ et al. Benchmark of Schemes for Multiscale Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 2015 Apr;11(4):1389-1398. https://doi.org/10.1021/ct501102b


BibTeX

@article{6b1cda352b2e46e6a0edce94aa4fa41c,
title = "Benchmark of Schemes for Multiscale Molecular Dynamics Simulations",
abstract = "In multiscale molecular dynamics simulations the accuracy of detailed models is combined with the efficiency of a reduced representation. For several applications - namely those of sampling enhancement - it is desirable to combine fine-grained (FG) and coarse-grained (CG) approaches into a single hybrid approach with an adjustable mixing parameter. We present a benchmark of three algorithms that use a mixing of the two representation layers using a Lagrangian formalism. The three algorithms use three different approaches for keeping the particles at the FG level of representation together: 1) addition of forces, 2) mass scaling, and 3) temperature scaling. The benchmark is applied to liquid hexadecane and includes an evaluation of the average configurational entropy of the FG and CG subsystems. The temperature-scaling scheme achieved a 3-fold sampling speedup with little deviation of FG properties. The addition-of-forces scheme kept FG properties the best but provided little sampling speedup. The mass-scaling scheme yielded a 5-fold speedup but deviated the most from FG properties.",
keywords = "BIOMOLECULAR SIMULATIONS, ALGORITHMS, POTENTIALS, EFFICIENT, SYSTEMS, MODELS",
author = "N. Goga and Melo, {M. N.} and Rzepiela, {A. J.} and {de Vries}, Alex and A. Hadar and Marrink, {S. J.} and Herman Berendsen",
year = "2015",
month = apr,
doi = "10.1021/ct501102b",
language = "English",
volume = "11",
pages = "1389--1398",
journal = "Journal of Chemical Theory and Computation",
issn = "1549-9618",
publisher = "AMER CHEMICAL SOC",
number = "4",

}

RIS

TY - JOUR

T1 - Benchmark of Schemes for Multiscale Molecular Dynamics Simulations

AU - Goga, N.

AU - Melo, M. N.

AU - Rzepiela, A. J.

AU - de Vries, Alex

AU - Hadar, A.

AU - Marrink, S. J.

AU - Berendsen, Herman

PY - 2015/4

Y1 - 2015/4

N2 - In multiscale molecular dynamics simulations the accuracy of detailed models is combined with the efficiency of a reduced representation. For several applications - namely those of sampling enhancement - it is desirable to combine fine-grained (FG) and coarse-grained (CG) approaches into a single hybrid approach with an adjustable mixing parameter. We present a benchmark of three algorithms that use a mixing of the two representation layers using a Lagrangian formalism. The three algorithms use three different approaches for keeping the particles at the FG level of representation together: 1) addition of forces, 2) mass scaling, and 3) temperature scaling. The benchmark is applied to liquid hexadecane and includes an evaluation of the average configurational entropy of the FG and CG subsystems. The temperature-scaling scheme achieved a 3-fold sampling speedup with little deviation of FG properties. The addition-of-forces scheme kept FG properties the best but provided little sampling speedup. The mass-scaling scheme yielded a 5-fold speedup but deviated the most from FG properties.

AB - In multiscale molecular dynamics simulations the accuracy of detailed models is combined with the efficiency of a reduced representation. For several applications - namely those of sampling enhancement - it is desirable to combine fine-grained (FG) and coarse-grained (CG) approaches into a single hybrid approach with an adjustable mixing parameter. We present a benchmark of three algorithms that use a mixing of the two representation layers using a Lagrangian formalism. The three algorithms use three different approaches for keeping the particles at the FG level of representation together: 1) addition of forces, 2) mass scaling, and 3) temperature scaling. The benchmark is applied to liquid hexadecane and includes an evaluation of the average configurational entropy of the FG and CG subsystems. The temperature-scaling scheme achieved a 3-fold sampling speedup with little deviation of FG properties. The addition-of-forces scheme kept FG properties the best but provided little sampling speedup. The mass-scaling scheme yielded a 5-fold speedup but deviated the most from FG properties.

KW - BIOMOLECULAR SIMULATIONS

KW - ALGORITHMS

KW - POTENTIALS

KW - EFFICIENT

KW - SYSTEMS

KW - MODELS

U2 - 10.1021/ct501102b

DO - 10.1021/ct501102b

M3 - Article

VL - 11

SP - 1389

EP - 1398

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

SN - 1549-9618

IS - 4

ER -

ID: 22983244