ArticleBiomolecules2021
Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.
Article in Biomolecules, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed.
- Coarse-graining analysis for non-invasive, label-free, and quantitative evaluation of undulating motion in cultured oral mucosa epithelial cell sheets.Regenerative therapy · 2026Article
- Coarse-Graining Reshapes Knot Dynamics in Polymers and Proteins.The journal of physical chemistry. B · 2026Article
- Artificial intelligence and ultra-high performance computing methods and experiments for drug discovery: virtual screening, deep learning, molecular dynamics simulations, ADMET modelling, and experimental validation.Molecular biomedicine · 2026Review
- Multiscale frameworks for exploring protein energy landscapes: advances in theory and simulation.Journal of biological physics · 2026Review
- Learning data-efficient coarse-grained molecular dynamics from forces and noise.Nature communications · 2026Article
- Molecular dynamics simulations reveal DNA gate opening mechanisms for M. smegmatis topoisomerase 1A.Biophysical journal · 2026Article
- Molecular dynamics simulation in traditional Chinese medicine research: from molecular mechanisms to multiscale validation.Frontiers in chemistry · 2026Review
- Decoding Solubility Signatures from Amyloid Monomer Energy Landscapes.Journal of chemical theory and computation · 2025Article
- Extending the Martini 3 Coarse-Grained Force Field to Hyaluronic Acid.The journal of physical chemistry. B · 2025Article
- Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field.Journal of chemical information and modeling · 2025Article
- Secondary Structure in Free and Assisted Modeling of Proteins with the Coarse-Grained UNRES Force Field.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Advanced Membrane Simulations in Probiotics and Gut Microbiome Interaction Research: The Current Trends and Insights.Current pharmaceutical design · 2025Review
- Assessment of Four Theoretical Approaches to Predict Protein Flexibility in the Crystal Phase and Solution.Journal of chemical theory and computation · 2024Article
- Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics.International journal of molecular sciences · 2024Review
- Making the cut: Multiscale simulation of membrane remodeling.Current opinion in structural biology · 2024Review
- Analysis of proteins in the light of mutations.European biophysics journal : EBJ · 2024Review
- Multilevel Framework for Analysis of Protein Folding Involving Disulfide Bond Formation.The journal of physical chemistry. B · 2024Article
- Exploring Free Energies of Specific Protein Conformations Using the Martini Force Field.Journal of chemical theory and computation · 2024Article
- Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin.Journal of chemical theory and computation · 2023Article
- Protein structure prediction from the complementary science perspective.Biophysical reviews · 2023Article
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Authors and funding
6 authors.
Funding
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Abstract
Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications of coarse-grained molecular dynamics. We demonstrate that the motion of coarse-grained sites is governed by the potential of mean force and the friction and stochastic forces, resulting from integrating out the secondary degrees of freedom. Consequently, Langevin dynamics is a natural means of describing the motion of a system at the coarse-grained level and the potential of mean force is the physical basis of the coarse-grained force fields. Moreover, the choice of coarse-grained variables and the fact that coarse-grained sites often do not have spherical symmetry implies a non-diagonal inertia tensor. We describe selected coarse-grained models used in molecular dynamics simulations, including the most popular MARTINI model developed by Marrink's group and the UNICORN model of biological macromolecules developed in our laboratory. We conclude by discussing examples of the application of coarse-grained molecular dynamics to study biologically important processes.
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