A polarizable coarse-grained water model for coarse-grained proteins simulations
A polarizable coarse-grained water model for coarse-grained proteins simulations
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DOI：
10.1016/j.cplett.2008.11.092
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发表时间：
2009-01-13
影响因子：
2.8
通讯作者：
Borgis, Daniel
中科院分区：
文献类型：
--
作者：
Ha-Duong, Tap;Basdevant, Nathalie;Borgis, Daniel
为了描述粗粒分子动力学模拟中的溶剂化效应，引入了一个数值效率较高的粗粒水模型。溶剂由嵌入三个水分子的可极化伪粒子表示。粒子携带感应偶极子，这些偶极子对溶质电场敏感，但彼此不敏感。溶剂模型是兼容的粗粒蛋白质力场涉及每个残留物的颗粒数量减少，并产生定量描述的溶剂化特性，如疏水力和静电溶剂化自由能。这些后期的数量可以在短的模拟窗口内进行“动态”估计。(C)2008年爱思唯尔B。版权所有© 2016
To describe solvation effects in coarse-grained molecular dynamics simulations, a numerically efficient coarse-grained water model is introduced. The solvent is represented by polarizable pseudo-particles embedding three water molecules. The particles carry induced dipoles that are made sensitive to the solute electric field, but not to each other. The solvent model is compatible with a coarse-grained proteins force field involving a reduced number of grains per residue and yields quantitative description of solvation properties, such as hydrophobic forces and electrostatic solvation free-energies. Those later quantities can be estimated 'on-the-fly' over short simulation windows. (C) 2008 Elsevier B. V. All rights reserved.