ArticleThe Journal of chemical physics2008
The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models.
Article in The Journal of chemical physics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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76 citing papers in PubMed.
- Structure and Dynamics of the HIV-1 Envelope Protein on the Virion Envelope.Journal of the American Chemical Society · 2026Article
- NNP/CG-MM: Embedding of All-Atom Neural Network Potentials into a Coarse-Grained Molecular Mechanics Environment.Journal of chemical theory and computation · 2026Article
- Collective fluctuations underlying nanobody inhibitory activity targetingbioRxiv : the preprint server for biology · 2026Article
- Structure and Dynamics of the HIV-1 Envelope Protein on the Virion Envelope.bioRxiv : the preprint server for biology · 2026Article
- Probabilistic Forecasting for Coarse-Grained Molecular Dynamics.Journal of chemical theory and computation · 2026Article
- Lattice instability drives formation of protofilament clusters at the microtubule plus-end tips.Biophysical journal · 2026Article
- Progressive Backmapping of Highly Coarse-Grained Protein Models.bioRxiv : the preprint server for biology · 2026Article
- Graph Neural Networks for Polymer Characterization and Property Prediction: Opportunities and Challenges.Journal of chemical information and modeling · 2026Review
- Bottom-up Coarse-Grained Models of Asymmetric Membranes.The journal of physical chemistry. B · 2025Article
- Approximation of Anisotropic Pair Potentials Using Multivariate Interpolation.The journal of physical chemistry. B · 2025Article
- MSBack: Multiscale Backmapping of Highly Coarse-Grained Proteins Using Constrained Diffusion.Journal of chemical theory and computation · 2025Article
- A Hybrid Bottom-Up and Data-Driven Machine Learning Approach for Accurate Coarse-Graining of Large Molecular Complexes.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
- Enhancing the Assembly Properties of Bottom-Up Coarse-Grained Phospholipids.Journal of chemical theory and computation · 2024Article
- Changing Your Martini Can Still Give You a Hangover.Journal of chemical theory and computation · 2024Article
- Multiscale modelling of transport in polymer-based reverse-osmosis/nanofiltration membranes: present and future.Discover nano · 2024Review
- Coarse-Graining with Equivariant Neural Networks: A Path Toward Accurate and Data-Efficient Models.The journal of physical chemistry. B · 2023Article
- OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining.The journal of physical chemistry. B · 2023Article
- Automatic identification of chemical moieties.Physical chemistry chemical physics : PCCP · 2023Article
16 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MS-CG variational principle determines the exact many-body potential of mean force (PMF) governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MS-CG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the many-body PMF. The present paper applies the MS-CG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this many-body PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a one-site CG model of methanol and a molecular CG model of the EMIM(+)NO(3) (-) ionic liquid are provided to illustrate the method.
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