There are various flows inside and outside cells in vivo. Nonequilibrium molecular dynamics (NEMD) simulation is a useful tool for understanding the effects of these flows on the dynamics of biomolecules. We propose an NEMD method to generate a Poiseuille-like flow between lipid bilayers. We extended the conventional equilibrium MD method to produce a flow by adding constant external force terms to the water molecules. Using the Lagrange multiplier method, the center of mass of the lipid bilayer is constrained so that the flow does not sweep away the lipid bilayer, but the individual lipid molecules fluctuate. The temperature of the system is controlled properly in the solution and membrane by using the Nosé-Hoover thermostat. We found that the flow velocity increases linearly as the applied external force term increases. It is possible to estimate the appropriate value of acceleration to generate a flow with an arbitrary velocity using this proportional relation once a single short MD simulation is performed. We also found that the flow between two lipid bilayers is slower than the analytical solution of the Navier-Stokes equations between rigid parallel plates due to the interactions between water molecules and the membrane. This method can be applied not only to a flow on lipid membranes but also to a flow on soft surfaces generally.

中文翻译：

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在脂质双层之间产生泊肃叶样流动的非平衡分子动力学方法。


体内细胞内外有各种流动。非平衡分子动力学 （NEMD） 模拟是了解这些流动对生物分子动力学影响的有用工具。我们提出了一种 NEMD 方法，在脂质双层之间产生泊肃叶样流动。我们扩展了传统的平衡 MD 方法，通过向水分子添加恒定的外力项来产生流动。使用拉格朗日乘子法，脂质双层的质心受到约束，因此流动不会冲走脂质双层，但单个脂质分子会波动。通过使用 Nosé-Hoover 恒温器，系统的温度在溶液和膜中得到适当控制。我们发现，随着施加的外力项的增加，流速呈线性增加。一旦执行了单个短 MD 仿真，就可以使用这种比例关系估计适当的加速度值，以生成具有任意速度的流动。我们还发现，由于水分子和膜之间的相互作用，两个脂质双层之间的流动比刚性平行板之间 Navier-Stokes 方程的解析解慢。这种方法不仅可以应用于脂质膜上的流动，还可以应用于一般软表面上的流动。