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-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.
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Switzerland.
Sereina
S
Riniker
Jane R
JR
Allison
Wilfred F
WF
van Gunsteren
D003198:Computer Simulation; D004058:Diffusion; D008954:Models, Biological; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
D012997:Solvents