On developing coarse-grained models for biomolecular simulation: a review

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-essent...

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Bibliographic Details
Published in:Physical chemistry chemical physics : PCCP 2012-09, Vol.14 (36), p.12423-1243
Main Authors: Riniker, Sereina, Allison, Jane R, van Gunsteren, Wilfred F
Format: Article
Language:English
Subjects:
Chemistry
Coarsening
Computer Simulation
Degrees of freedom
Diffusion
Exact sciences and technology
General and physical chemistry
Mathematical analysis
Modelling
Models, Biological
Preserves
Readers
Solvents - chemistry
Thermodynamics
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Summary: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. A review of the basic ingredients of developing coarse-grained models and conditions to be satisfied for preserving the correct physical mechanisms.
ISSN:1463-9076
1463-9084
DOI:10.1039/c2cp40934h