Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Switzerland.
Phys Chem Chem Phys. 2012 Sep 28;14(36):12423-30. doi: 10.1039/c2cp40934h. Epub 2012 Jun 8.
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.
所谓的粗粒化模型是一种用于模拟生物分子过程中长时间尺度的流行模型类型。与原子模型相比，这种模型是粗粒化的。但是，任何对过程或物质的建模都涉及到粗粒化，即从更细粒度的建模水平中消除非必要的自由度和相互作用。本文回顾了基于细粒度模型特性开发粗粒化模型的基本要素，以及为了在粗粒化过程中保留正确的物理机制必须满足的条件。这篇综述应该有助于读者确定生物分子系统的粗粒化模型有多现实，即它是否反映了潜在的物理机制，还是仅仅提供了感兴趣的过程或物质的一组漂亮图片。
