ArticleThe journal of physical chemistry letters2019
Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability.
Article in The journal of physical chemistry letters, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Analytical coarse grained potential parameterization by reinforcement learning for anisotropic cellulose.Journal of molecular modeling · 2026Article
- Development of Coarse-Grained Lipid Force Fields Based on a Graph Neural Network.Journal of chemical theory and computation · 2025Article
- Understanding the coarse-grained free energy landscape of phospholipids and their phase separation.Biophysical journal · 2025Article
- Thermodynamic Transferability in Coarse-Grained Force Fields Using Graph Neural Networks.Journal of chemical theory and computation · 2024Article
- Changing Your Martini Can Still Give You a Hangover.Journal of chemical theory and computation · 2024Article
- Chemically Specific Systematic Coarse-Grained Polymer Model with Both Consistently Structural and Dynamical Properties.JACS Au · 2024Article
- OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining.The journal of physical chemistry. B · 2023Article
- Machine learned coarse-grained protein force-fields: Are we there yet?Current opinion in structural biology · 2023Review
- Slicing and Dicing: Optimal Coarse-Grained Representation to Preserve Molecular Kinetics.ACS central science · 2023Article
- Statistical Mechanical Design Principles for Coarse-Grained Interactions across Different Conformational Free Energy Surfaces.The journal of physical chemistry letters · 2023Article
- Bottom-up Coarse-Graining: Principles and Perspectives.Journal of chemical theory and computation · 2022Review
- Coarse-Grained Water Model Development for Accurate Dynamics and Structure Prediction.ACS omega · 2022Article
- Inositol Hexakisphosphate (IP6) Accelerates Immature HIV-1 Gag Protein Assembly toward Kinetically Trapped Morphologies.Journal of the American Chemical Society · 2022Article
- Accurate model of liquid-liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Coarse-Grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding of the Origins of a MARTINI Hangover.Journal of chemical theory and computation · 2021Article
- A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). II. Temperature transferability and structural properties at low temperature.The Journal of chemical physics · 2021Article
- A Deep Graph Network-Enhanced Sampling Approach to Efficiently Explore the Space of Reduced Representations of Proteins.Frontiers in molecular biosciences · 2021Article
- Article
- An Information-Theory-Based Approach for Optimal Model Reduction of Biomolecules.Journal of chemical theory and computation · 2020Article
- Temperature and Phase Transferable Bottom-up Coarse-Grained Models.Journal of chemical theory and computation · 2020Article
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3 authors.
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Abstract
Coarse-grained (CG) models facilitate efficient simulation of complex systems by integrating out the atomic, or fine-grained (FG), degrees of freedom. Systematically derived CG models from FG simulations often attempt to approximate the CG potential of mean force (PMF), an inherently multidimensional and many-body quantity, using additive pairwise contributions. However, they currently lack fundamental principles that enable their extensible use across different thermodynamic state points, i.e., transferability. In this work, we investigate the explicit energy-entropy decomposition of the CG PMF as a means to construct transferable CG models. In particular, despite its high-dimensional nature, we find for liquid systems that the entropic component to the CG PMF can similarly be represented using additive pairwise contributions, which we show is highly coupled to the CG configurational entropy. This approach formally connects the missing entropy that is lost due to the CG representation, i.e., translational, rotational, and vibrational modes associated with the missing degrees of freedom, to the CG entropy. By design, the present framework imparts transferable CG interactions across different temperatures due to the explicit definition of an additive entropic contribution. Furthermore, we demonstrate that transferability across composition state points, such as between bulk liquids and their mixtures, is also achieved by designing combining rules to approximate cross-interactions from bulk CG PMFs. Using the predicted CG model for liquid mixtures, structural correlations of the fitted CG model were found to corroborate a high-fidelity combining rule. Our findings elucidate the physical nature and compact representation of CG entropy and suggest a new approach for overcoming the transferability problem. We expect that this approach will further extend the current view of CG modeling into predictive multiscale modeling.
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