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