Robertson Alex, Luttmann Edgar, Pande Vijay S
Department of Chemistry, Stanford University, Stanford, California 94305, USA.
J Comput Chem. 2008 Apr 15;29(5):694-700. doi: 10.1002/jcc.20828.
Molecular dynamics simulations are a useful tool for characterizing protein folding pathways. There are several methods of treating electrostatic forces in these simulations with varying degrees of physical fidelity and computational efficiency. In this article, we compare the reaction field (RF) algorithm, particle-mesh Ewald (PME), and tapered cutoffs with increasing cutoff radii to address the impact of the electrostatics method employed on the folding kinetics. We quantitatively compare different methods by a correlation of quantitative measures of protein folding kinetics. The results of these comparisons show that for protein folding kinetics, the RF algorithm can quantitatively reproduce the kinetics of the more costly PME algorithm. These results not only assist the selection of appropriate algorithms for future simulations, but also give insight on the role that long-range electrostatic forces have in protein folding.
分子动力学模拟是表征蛋白质折叠途径的一种有用工具。在这些模拟中，有几种处理静电力的方法，其物理逼真度和计算效率各不相同。在本文中，我们比较了反应场（RF）算法、粒子网格埃瓦尔德（PME）算法以及随着截止半径增加的锥形截止方法，以探讨所采用的静电方法对折叠动力学的影响。我们通过蛋白质折叠动力学定量测量的相关性来定量比较不同方法。这些比较结果表明，对于蛋白质折叠动力学，RF算法能够定量重现成本更高的PME算法的动力学。这些结果不仅有助于为未来的模拟选择合适的算法，还能深入了解长程静电力在蛋白质折叠中所起的作用。
