ArticleJournal of chemical theory and computation2020
Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange.
Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field.Journal of chemical information and modeling · 2025Article
- Understanding the free-energy landscape of phase separation in lipid bilayers using molecular dynamics.Biophysical journal · 2023Article
- Understanding the Free Energy Landscape of Phase Separation in Lipid Bilayers using Molecular Dynamics.bioRxiv : the preprint server for biology · 2023Article
- Mutational Impacts on the N and C Terminal Domains of the MUC5B Protein: A Transcriptomics and Structural Biology Study.ACS omega · 2023Article
- Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions.Biomolecules · 2021Review
- Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations.Journal of chemical theory and computation · 2021Article
- Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.Biomolecules · 2021Article
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Authors and funding
5 authors.
Funding
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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.
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Registered trials
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