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关于在施加表面张力的情况下模拟脂质双层:周期性边界条件和波动

On simulating lipid bilayers with an applied surface tension: periodic boundary conditions and undulations.

作者信息

Feller S E, Pastor R W

机构信息

Biophysics Laboratory, Food and Drug Administration, Rockville, Maryland 20852-1448, USA.

出版信息

Biophys J. 1996 Sep;71(3):1350-5. doi: 10.1016/S0006-3495(96)79337-2.

Abstract

As sketched in Fig. 1, a current molecular dynamics computer simulation of a lipid bilayer fails to capture significant features of the macroscopic system, including long wavelength undulations. Such fluctuations are intrinsically connected to the value of the macroscopic (or thermodynamic) surface tension (cf. Eqs. 1 and 9; for a related treatment, see Brochard et al., 1975, 1976). Consequently, the surface tension that might be evaluated in an MD simulation should not be expected to equal the surface tension obtained from macroscopic measurements. Put another way, the largest of the three simulations presented here contained over 16,000 atoms and required substantial computer time to complete, but modeled a system of only 36 lipids per side. From this perspective it is not surprising that the system is not at the thermodynamic limit. An important practical consequence of this effect is that simulations with fluctuating area should be carried out with a nonzero applied surface tension (gamma 0 of Fig. 2) even when the macroscopic tension is zero, or close to zero. Computer simulations at fixed surface area, which can explicitly determine pressure anisotropy at the molecular level, should ultimately lend insight into the value of gamma 0, including its dependence on lipid composition and other membrane components. As we have noted and will describe further in separate publications (Feller et al., 1996; Feller et al., manuscript in preparation), surface tensions obtained from simulations can be distorted by inadequate initial conditions and convergence, and are sensitive to potential energy functions, force truncation methods, and system size; it is not difficult, in fact, to tune terms in the potential energy function so as to yield surface tensions close to zero. This is why parameters should be tested extensively on simpler systems, for example, monolayers. The estimates of gamma 0 that we have presented here should be regarded as qualitative, and primarily underscore the assertion that the surface tension of a microscopically flat, simulation-sized patch is significantly greater than zero. As the simulation cell length increases, the surface tension that would be evaluated (or should be applied) decreases; in the limit of micrometer-sized simulation cells, gamma would approach zero or its appropriate thermodynamic value. The theories presented here also imply that the estimation of bilayer surface tension from monolayer data should take the degree of flatness into account. These conclusions are independent of the precise values of parameters such as bending constants. In conclusion, from the simulator's perspective, the question "What is the surface tension of a bilayer?" is better phrased as "What is the value of the applied surface tension necessary to simulate a particular experimental system with a given number of lipids?". As we have shown, the answer to the second question varies, but it should not be assumed a priori to equal zero.

摘要

如图1所示,当前对脂质双层的分子动力学计算机模拟无法捕捉宏观系统的显著特征,包括长波长波动。这种波动与宏观(或热力学)表面张力的值有着内在联系(参见方程1和9;相关论述见Brochard等人,1975年、1976年)。因此,不应期望在分子动力学模拟中评估得到的表面张力与从宏观测量中获得的表面张力相等。换句话说,这里展示的三个模拟中规模最大的一个包含超过16000个原子,完成模拟需要大量计算机时间,但它模拟的系统每侧仅有36个脂质分子。从这个角度来看,该系统未达到热力学极限也就不足为奇了。这种效应的一个重要实际后果是,即使宏观张力为零或接近零,对于面积波动的模拟也应在非零的外加表面张力(图2中的γ0)下进行。在固定表面积下的计算机模拟能够在分子水平明确确定压力各向异性,最终应该有助于深入了解γ0的值,包括其对脂质组成和其他膜成分的依赖性。正如我们已经指出并将在单独的出版物中进一步描述的那样(Feller等人,1996年;Feller等人,正在准备的手稿),从模拟中获得的表面张力可能会因初始条件不足和收敛问题而失真,并且对势能函数、力截断方法和系统大小敏感;实际上,调整势能函数中的项以得到接近零的表面张力并不困难。这就是为什么应该在更简单的系统(例如单层膜)上广泛测试参数的原因。我们在此给出的γ0估计值应被视为定性的,主要是为了强调这样一个观点,即微观上平整的、模拟规模大小的膜片的表面张力显著大于零。随着模拟单元长度增加,所评估(或应施加)的表面张力会降低;在微米级模拟单元的极限情况下,γ将接近零或其适当的热力学值。这里提出的理论还意味着,从单层数据估计双层表面张力时应考虑平整度。这些结论与诸如弯曲常数等参数的精确值无关。总之,从模拟者的角度来看,“双层膜的表面张力是多少?”这个问题更好的表述是“对于给定数量脂质的特定实验系统进行模拟,所需施加的表面张力的值是多少?”。正如我们所展示的,第二个问题的答案各不相同,但不应先验地假定其等于零。

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