ArticleThe Journal of chemical physics2021
A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model.
Article in The Journal of chemical physics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- NNP/CG-MM: Embedding of All-Atom Neural Network Potentials into a Coarse-Grained Molecular Mechanics Environment.Journal of chemical theory and computation · 2026Article
- Mapping Still Matters: Coarse-Graining with Machine Learning Potentials.Journal of chemical information and modeling · 2026Article
- Density- and Temperature-Dependent Potentials: Redefinition of the Local Density to Improve the Simulation of Liquids within Generalized Dissipative Particle Dynamics.Journal of chemical theory and computation · 2026Article
- Coarse-Graining with Equivariant Neural Networks: A Path Toward Accurate and Data-Efficient Models.The journal of physical chemistry. B · 2023Article
- Coarse-Graining Waters: Unveiling The Effective Hydrophilicity/Hydrophobicity of Individual Protein Atoms and The Roles of Waters' Hydrogens.Journal of chemical theory and computation · 2023Article
- OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining.The journal of physical chemistry. B · 2023Article
- Utilizing Machine Learning to Greatly Expand the Range and Accuracy of Bottom-Up Coarse-Grained Models through Virtual Particles.Journal of chemical theory and computation · 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
- Anisotropic Electrostatic Interactions in Coarse-Grained Water Models to Enhance the Accuracy and Speed-Up Factor of Mesoscopic Simulations.The journal of physical chemistry. B · 2021Article
- "Dividing and Conquering" and "Caching" in Molecular Modeling.International journal of molecular sciences · 2021Review
- 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
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Authors and funding
4 authors.
Funding
Abstract
Water is undoubtedly one of the most important molecules for a variety of chemical and physical systems, and constructing precise yet effective coarse-grained (CG) water models has been a high priority for computer simulations. To recapitulate important local correlations in the CG water model, explicit higher-order interactions are often included. However, the advantages of coarse-graining may then be offset by the larger computational cost in the model parameterization and simulation execution. To leverage both the computational efficiency of the CG simulation and the inclusion of higher-order interactions, we propose a new statistical mechanical theory that effectively projects many-body interactions onto pairwise basis sets. The many-body projection theory presented in this work shares similar physics from liquid state theory, providing an efficient approach to account for higher-order interactions within the reduced model. We apply this theory to project the widely used Stillinger-Weber three-body interaction onto a pairwise (two-body) interaction for water. Based on the projected interaction with the correct long-range behavior, we denote the new CG water model as the Bottom-Up Many-Body Projected Water (BUMPer) model, where the resultant CG interaction corresponds to a prior model, the iteratively force-matched model. Unlike other pairwise CG models, BUMPer provides high-fidelity recapitulation of pair correlation functions and three-body distributions, as well as N-body correlation functions. BUMPer extensively improves upon the existing bottom-up CG water models by extending the accuracy and applicability of such models while maintaining a reduced computational cost.
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Registered trials
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