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

Multi-scale

Enhanced sampling

Solvents

Journal article

Methods

Author

Yang Liu, Weria Pezeshkian, Jonathan Barnoud, Alex H de Vries, Siewert J Marrink

Doi

https://doi.org/10.1021/acs.jctc.0c00429

Citation (APA 7)

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.

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.