Comparing simulated and experimental translation and rotation constants: range of validity for viscosity scaling.
Comparing simulated and experimental translation and rotation constants: range of validity for viscosity scaling.
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比较模拟和平移和旋转常数与实验：粘度缩放的有效性范围。
DOI：
10.1021/jp105549s
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发表时间：
2010
期刊：
影响因子：
--
通讯作者：
Pastor,RichardW
中科院分区：
文献类型：
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作者：
Venable,RichardM;Hatcher,Elizabeth;Guvench,Olgun;MackerellJr,AlexanderD;Pastor,RichardW
正确模拟动态特性（包括分子扩散）是经验力场的一个重要目标。然而，广泛使用的TIP3P水模型并不能再现水的实验粘度。因此，需要对水溶液中溶质的模拟扩散常数进行缩放，以便有效地将它们与实验进行比较。有人提出，在模拟和实验溶液粘度的浓度依赖性平行的情况下，按模型和真实水的粘度比率进行缩放是适当的。通过该 ansatz，可以对葡萄糖和海藻糖进行高达 20 wt% 的粘度缩放，以使用 CHARMM 添加剂碳水化合物力场 C35 和 TIP3P 水进行模拟；高于此值，模拟粘度的浓度依赖性滞后于实验，不建议缩放。葡萄糖和低浓度二糖海藻糖、麦芽糖和蜜二糖的缩放平移扩散常数与实验几乎在定量上一致，葡萄糖、海藻糖和麦芽糖的NMR13CT1也是如此；这些结果支持使用 C35 来模拟低浓度下的糖转运特性。在高浓度下，葡萄糖和海藻糖的缩放扩散常数分别低估和高估了实验。水动力珠模型计算表明葡萄糖的水合水平约为 1 个水/羟基。二糖的模式更为复杂，尽管根据分析，海藻糖比麦芽糖多结合 0.5 到 1 的水。
Proper simulation of dynamic properties, including molecular diffusion, is an important goal of empirical force fields. However, the widely used TIP3P water model does not reproduce the experimental viscosity of water. Consequently, scaling of simulated diffusion constants of solutes in aqueous solutions is required to effectively compare them with experiment. It is proposed that scaling by the ratio of viscosities of model and real water is appropriate in the regime where the concentration dependence of simulated and experimental solution viscosities is parallel. With this ansatz, viscosity scaling can be carried out for glucose and trehalose up to 20 wt % for simulations carried out with the CHARMM additive carbohydrate force field C35 and TIP3P water; above this value, the concentration dependence of simulated viscosities lags that of experiment, and scaling is not advised. Scaled translational diffusion constants for glucose and the disaccharides trehalose, maltose, and melibiose at low concentration agree nearly quantitatively with experiment, as do NMR13CT1’s for glucose, trehalose, and maltose; these results support the use of C35 for simulations of sugar transport properties at low concentration. At high concentrations the scaled diffusion constants for glucose and trehalose underestimate and overestimate experiment, respectively. Hydrodynamic bead model calculations indicate a hydration level of approximately 1 water/hydroxyl for glucose. Patterns for the disaccharides are more complicated, though trehalose binds 0.5 to 1 more water than does maltose depending on the analysis.