Giupponi G, De Fabritiis G, Coveney Peter V
Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London, UK.
J Chem Phys. 2007 Apr 21;126(15):154903. doi: 10.1063/1.2720385.
We present a hybrid computational method for simulating the dynamics of macromolecules in solution which couples a mesoscale solver for the fluctuating hydrodynamics (FH) equations with molecular dynamics to describe the macromolecule. The two models interact through a dissipative Stokesian term first introduced by Ahlrichs and Dunweg [J. Chem. Phys. 111, 8225 (1999)]. We show that our method correctly captures the static and dynamical properties of polymer chains as predicted by the Zimm model. In particular, we show that the static conformations are best described when the ratio sigma/b=0.6, where sigma is the Lennard-Jones length parameter and b is the monomer bond length. We also find that the decay of the Rouse modes' autocorrelation function is better described with an analytical correction suggested by Ahlrichs and Dunweg. Our FH solver permits us to treat the fluid equation of state and transport parameters as direct simulation parameters. The expected independence of the chain dynamics on various choices of fluid equation of state and bulk viscosity is recovered, while excellent agreement is found for the temperature and shear viscosity dependence of center of mass diffusion between simulation results and predictions of the Zimm model. We find that Zimm model approximations start to fail when the Schmidt number Sc < or approximately 30. Finally, we investigate the importance of fluid fluctuations and show that using the preaveraged approximation for the hydrodynamic tensor leads to around 3% error in the diffusion coefficient for a polymer chain when the fluid discretization size is greater than 50 A.
我们提出了一种混合计算方法，用于模拟溶液中大分子的动力学，该方法将用于波动流体动力学（FH）方程的中尺度求解器与分子动力学相结合来描述大分子。这两个模型通过Ahlrichs和Dunweg [《化学物理杂志》111, 8225 (1999)]首次引入的耗散斯托克斯项相互作用。我们表明，我们的方法能够正确捕捉齐姆模型预测的聚合物链的静态和动态特性。特别是，我们表明当σ/b = 0.6时，静态构象得到了最好的描述，其中σ是 Lennard-Jones 长度参数，b是单体键长。我们还发现，使用Ahlrichs和Dunweg建议的解析修正可以更好地描述劳斯模式自相关函数的衰减。我们的FH求解器使我们能够将流体状态方程和输运参数视为直接模拟参数。恢复了链动力学对流体状态方程和本体粘度各种选择的预期独立性，同时在模拟结果与齐姆模型预测之间，发现质心扩散的温度和剪切粘度依赖性具有极好的一致性。我们发现，当施密特数Sc≤或约为30时，齐姆模型近似开始失效。最后，我们研究了流体涨落的重要性，并表明当流体离散化尺寸大于50 Å时，对流体动力学张量使用预平均近似会导致聚合物链扩散系数产生约3%的误差。
