Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Switzerland.
J Chem Phys. 2012 Jul 28;137(4):044120. doi: 10.1063/1.4739068.
The use of a supra-molecular coarse-grained (CG) model for liquid water as solvent in molecular dynamics simulations of biomolecules represented at the fine-grained (FG) atomic level of modelling may reduce the computational effort by one or two orders of magnitude. However, even if the pure FG model and the pure CG model represent the properties of the particular substance of interest rather well, their application in a hybrid FG/CG system containing varying ratios of FG versus CG particles is highly non-trivial, because it requires an appropriate balance between FG-FG, FG-CG, and CG-CG energies, and FG and CG entropies. Here, the properties of liquid water are used to calibrate the FG-CG interactions for the simple-point-charge water model at the FG level and a recently proposed supra-molecular water model at the CG level that represents five water molecules by one CG bead containing two interaction sites. Only two parameters are needed to reproduce different thermodynamic and dielectric properties of liquid water at physiological temperature and pressure for various mole fractions of CG water in FG water. The parametrisation strategy for the FG-CG interactions is simple and can be easily transferred to interactions between atomistic biomolecules and CG water.
在以原子级别（FG）建模的精细模型（FG）中，使用超分子粗粒度（CG）模型作为溶剂进行生物分子的分子动力学模拟，可以将计算工作量减少一到两个数量级。然而，即使纯 FG 模型和纯 CG 模型可以很好地代表特定物质的性质，但将它们应用于包含不同 FG 与 CG 粒子比例的混合 FG/CG 系统中是非常复杂的，因为它需要在 FG-FG、FG-CG 和 CG-CG 能量以及 FG 和 CG 熵之间取得适当的平衡。在这里，使用液体水的性质来校准 FG 级别的简单点电荷水模型和 CG 级别的最近提出的超分子水模型之间的 FG-CG 相互作用，该模型用一个包含两个相互作用位点的 CG 珠表示五个水分子。对于不同摩尔分数的 CG 水在 FG 水中，只需两个参数即可重现生理温度和压力下液体水的不同热力学和介电性质。FG-CG 相互作用的参数化策略很简单，可以很容易地转移到原子生物分子和 CG 水之间的相互作用。
