Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange

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Standard

Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange. / Liu, Yang; Pezeshkian, Weria; Barnoud, Jonathan; de Vries, Alex H.; Marrink, Siewert J.

I: Journal of Chemical Theory and Computation, Bind 16, Nr. 8, 11.08.2020, s. 5313-5322.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Liu, Y, Pezeshkian, W, Barnoud, J, de Vries, AH & Marrink, SJ 2020, 'Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange', Journal of Chemical Theory and Computation, bind 16, nr. 8, s. 5313-5322. https://doi.org/10.1021/acs.jctc.0c00429

APA

Liu, Y., Pezeshkian, W., Barnoud, J., de Vries, A. H., & Marrink, S. J. (2020). Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange. Journal of Chemical Theory and Computation, 16(8), 5313-5322. https://doi.org/10.1021/acs.jctc.0c00429

Vancouver

Liu Y, Pezeshkian W, Barnoud J, de Vries AH, Marrink SJ. Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange. Journal of Chemical Theory and Computation. 2020 aug. 11;16(8):5313-5322. https://doi.org/10.1021/acs.jctc.0c00429

Author

Liu, Yang ; Pezeshkian, Weria ; Barnoud, Jonathan ; de Vries, Alex H. ; Marrink, Siewert J. / Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange. I: Journal of Chemical Theory and Computation. 2020 ; Bind 16, Nr. 8. s. 5313-5322.

Bibtex

@article{d9a973ae0c8e4ef18b23fe5e11764dab,
title = "Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange",
abstract = "The energy landscape of biomolecular systems contains many local minima that are separated by high energy barriers. Sampling this landscape in molecular dynamics simulations is a challenging task and often requires the use of enhanced sampling techniques. Here, we increase the sampling efficiency by coupling the fine-grained (FG) GROMOS force field to the coarse-grained (CG) Martini force field via the Hamiltonian replica exchange method (HREM). We tested the efficiency of this procedure using a lutein/octane system. In traditional simulations, cis-trans transitions of lutein are barely observed due to the high energy barrier separating these states. However, many of these transitions are sampled with our HREM scheme. The proposed method offers new possibilities for enhanced sampling of biomolecular conformations, making use of CG models without compromising the accuracy of the FG model.",
keywords = "MOLECULAR-DYNAMICS, BIOMOLECULAR SIMULATION, FORCE-FIELD, RESOLUTION, ALGORITHM, SYSTEMS",
author = "Yang Liu and Weria Pezeshkian and Jonathan Barnoud and {de Vries}, {Alex H.} and Marrink, {Siewert J.}",
year = "2020",
month = aug,
day = "11",
doi = "10.1021/acs.jctc.0c00429",
language = "English",
volume = "16",
pages = "5313--5322",
journal = "Journal of Chemical Theory and Computation",
issn = "1549-9618",
publisher = "American Chemical Society",
number = "8",

}

RIS

TY - JOUR

T1 - Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange

AU - Liu, Yang

AU - Pezeshkian, Weria

AU - Barnoud, Jonathan

AU - de Vries, Alex H.

AU - Marrink, Siewert J.

PY - 2020/8/11

Y1 - 2020/8/11

N2 - The energy landscape of biomolecular systems contains many local minima that are separated by high energy barriers. Sampling this landscape in molecular dynamics simulations is a challenging task and often requires the use of enhanced sampling techniques. Here, we increase the sampling efficiency by coupling the fine-grained (FG) GROMOS force field to the coarse-grained (CG) Martini force field via the Hamiltonian replica exchange method (HREM). We tested the efficiency of this procedure using a lutein/octane system. In traditional simulations, cis-trans transitions of lutein are barely observed due to the high energy barrier separating these states. However, many of these transitions are sampled with our HREM scheme. The proposed method offers new possibilities for enhanced sampling of biomolecular conformations, making use of CG models without compromising the accuracy of the FG model.

AB - The energy landscape of biomolecular systems contains many local minima that are separated by high energy barriers. Sampling this landscape in molecular dynamics simulations is a challenging task and often requires the use of enhanced sampling techniques. Here, we increase the sampling efficiency by coupling the fine-grained (FG) GROMOS force field to the coarse-grained (CG) Martini force field via the Hamiltonian replica exchange method (HREM). We tested the efficiency of this procedure using a lutein/octane system. In traditional simulations, cis-trans transitions of lutein are barely observed due to the high energy barrier separating these states. However, many of these transitions are sampled with our HREM scheme. The proposed method offers new possibilities for enhanced sampling of biomolecular conformations, making use of CG models without compromising the accuracy of the FG model.

KW - MOLECULAR-DYNAMICS

KW - BIOMOLECULAR SIMULATION

KW - FORCE-FIELD

KW - RESOLUTION

KW - ALGORITHM

KW - SYSTEMS

U2 - 10.1021/acs.jctc.0c00429

DO - 10.1021/acs.jctc.0c00429

M3 - Journal article

VL - 16

SP - 5313

EP - 5322

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

SN - 1549-9618

IS - 8

ER -

ID: 316753337