Publication

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

Liu, Y., Pezeshkian, W., Barnoud, J., De Vries, A. H. & Marrink, S. J., 2020, In : Journal of Chemical Theory and Computation. 16, 8, p. 5313-5322 10 p., acs.jctc.0c00429.

Research output: Contribution to journalArticleAcademicpeer-review

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.

Original languageEnglish
Article numberacs.jctc.0c00429
Pages (from-to)5313-5322
Number of pages10
JournalJournal of Chemical Theory and Computation
Volume16
Issue number8
Early online date22-Jun-2020
Publication statusPublished - 2020

    Keywords

  • MOLECULAR-DYNAMICS, BIOMOLECULAR SIMULATION, FORCE-FIELD, RESOLUTION, ALGORITHM, SYSTEMS

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