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Issue 36, 2012

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

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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.

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

Article information


Submitted
23 Mar 2012
Accepted
04 May 2012
First published
08 Jun 2012

Phys. Chem. Chem. Phys., 2012,14, 12423-12430
Article type
Perspective

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

S. Riniker, J. R. Allison and W. F. van Gunsteren, Phys. Chem. Chem. Phys., 2012, 14, 12423 DOI: 10.1039/C2CP40934H

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