Shear viscosity coefficient of acqueous glycerol from non-equilibrium Molecular Dynamics simulations

This dataset contains the results of non-equilibrium atomistic Molecular Dynamics simulations of water-glycerol liquid mixtures, at various relative concentrations. The goal of the simulations is to quantify the shear viscosity coefficient of said mixtures using the periodic perturbation technique [1]. 

The pattern "Glycerol***" refers to the mass fraction of glycerol ("000": pure water, "100": pure glycerol). Each folder contains three sets of simulations, with different perturbation force parameters ("Em*"), where configuration files necessary to reproduce molecular simulations simulations are provided. Maps of density and velocity field are in "Em*"->"Flow".

A small self-contained Python script to fit the velocity fields to a periodic cosine perturbation is provided (fit-periodic.py). Alternatively, viscosity can be obtained from energy outputs by running:

gmx energy -f ener.edr

and selecting "1/Viscosity". Simulations are performed with Gromacs. We refer to the code documentation for further information (https://manual.gromacs.org/).

References:

[1] B. Hess, Determining the shear viscosity of model liquids from molecular dynamics simulations, J. Chem. Phys. 116, 209–217 (2002) https://doi.org/10.1063/1.1421362

本数据集包含不同相对浓度下的水-甘油液态混合物的非平衡原子级分子动力学（Molecular Dynamics）模拟结果。本次模拟的目标是通过周期性微扰技术（periodic perturbation technique）[1]量化上述混合物的剪切粘度系数。

"Glycerol***"的命名格式代表甘油的质量分数：其中"000"代表纯水，"100"代表纯甘油。每个文件夹包含三组采用不同微扰力参数（"Em*"）的模拟实验，同时提供了复现该分子模拟所需的配置文件。密度场与速度场的映射文件存于"Em*"目录下的"Flow"子目录中。

本数据集附带了一款独立完整的Python脚本（fit-periodic.py），可用于将速度场拟合至周期性余弦微扰模型。此外，也可通过以下方式从能量输出文件中获取粘度值：运行命令`gmx energy -f ener.edr`并选择"1/Viscosity"选项。

本次模拟采用Gromacs软件完成，更多细节可参考其官方文档：https://manual.gromacs.org/。

参考文献：
[1] B. Hess. 从分子动力学模拟中确定模型液体的剪切粘度[J]. Journal of Chemical Physics, 2002, 116: 209–217. https://doi.org/10.1063/1.1421362