Journal ArticleDOI
On developing coarse-grained models for biomolecular simulation: a review.
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TLDR
This overview should help the reader to determine how realistic a coarse-grained model of a biomolecular system is, i.e. whether it reflects the underlying physical mechanisms or merely provides a set of pretty pictures of the process or substances of interest.Abstract:
So-called coarse-grained models are a popular type of model for accessing long time scales in simulations of biomolecular processes. Such models are coarse-grained with respect to atomic models. But any modelling of processes or substances involves coarse-graining, i.e. the elimination of non-essential degrees of freedom and interactions from a more fine-grained level of modelling. The basic ingredients of developing coarse-grained models based on the properties of fine-grained models are reviewed, together with the conditions that must be satisfied in order to preserve the correct physical mechanisms in the coarse-graining process. This overview should help the reader to determine how realistic a coarse-grained model of a biomolecular system is, i.e. whether it reflects the underlying physical mechanisms or merely provides a set of pretty pictures of the process or substances of interest.read more
Citations
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Journal ArticleDOI
Perspective: Coarse-grained models for biomolecular systems.
TL;DR: This review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network- based, native-centric, knowledge-based, and bottom-up modeling strategies.
Journal ArticleDOI
Coarse-Grained Protein Models and Their Applications
Sebastian Kmiecik,Dominik Gront,Michal Kolinski,Lukasz Wieteska,Lukasz Wieteska,Aleksandra Elzbieta Dawid,Andrzej Kolinski +6 more
TL;DR: An overview of coarse-grained models focusing on their design, including choices of representation, models of energy functions, sampling of conformational space, and applications in the modeling of protein structure, dynamics, and interactions are provided.
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Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations.
TL;DR: The extent to which current force fields reproduce (and fail to reproduce) certain relevant properties for which such comparisons are possible is examined.
Journal ArticleDOI
Modeling and Simulations of Polymers: A Roadmap
TL;DR: In this article, the authors discuss their philosophy for carefully developing or selecting appropriate models, performing, and analyzing polymer simulations, highlighting best practices, key challenges, and important advances in model development/selection, computational method choices, advanced sampling met...
Journal ArticleDOI
Metal Ion Modeling Using Classical Mechanics
Pengfei Li,Kenneth M. Merz +1 more
TL;DR: This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models, and valence bond-based models.
References
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The MARTINI force field : Coarse grained model for biomolecular simulations
TL;DR: An improved and extended version of the coarse grained lipid model is presented, coined the MARTINI force field, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds to reproduce the free energies of these chemical building blocks.
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Coarse grained model for semiquantitative lipid simulations
TL;DR: In this article, a coarse-grained (CG) model for lipid and surfactant systems is presented, where only a small number of coarse grained atom types interact using a few discrete levels of interaction.
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Algorithms for macromolecular dynamics and constraint dynamics
TL;DR: In this paper, the authors investigated the application of the computer simulation method of molecular dynamics to macromolecules and compared different algorithms for integrating the equations of motion, both theoretically and in practice.