Department of Physics and Astronomy, University of Sheffield, Sheffield, UK S3 7RH.
Phys Chem Chem Phys. 2009 Dec 7;11(45):10596-607. doi: 10.1039/b912067j. Epub 2009 Aug 18.
Different classical models for monovalent ions (typically used to neutralize proteins or nucleic acids) are available in the literature and are widely used in molecular dynamics simulations without a great knowledge of their quality, consistency with the macromolecular force field and impact on the global simulation results. In this paper the ability of several of the most popular ion models to reproduce both quantum mechanics and experimental results is examined. Artefacts due to the use of incorrect ion models in molecular dynamics simulations of concentrated solutions of NaCl and KCl in water and of a short DNA duplex in 500 mM aqueous solutions of NaCl and KCl have been analyzed. Our results allow us to discuss the robustness and reliability of different ion models and to highlight the source of potential errors arising from non-optimal models. However, it is also found that the structural and dynamic characteristics of DNA (as an example of a heavily charged macromolecule) in near-physiological conditions are quite independent of the ion model used, providing support to most already-published simulations of macromolecules.
不同的单价离子经典模型（通常用于中和蛋白质或核酸）在文献中已有报道，并且在分子动力学模拟中广泛使用，而人们对它们的质量、与大分子力场的一致性以及对全局模拟结果的影响知之甚少。本文研究了几种最流行的离子模型重现量子力学和实验结果的能力。分析了在 NaCl 和 KCl 水溶液中浓度较高的溶液以及在 500mM NaCl 和 KCl 水溶液中短 DNA 双链的分子动力学模拟中使用不正确的离子模型所产生的人为产物。我们的结果允许我们讨论不同离子模型的稳健性和可靠性，并突出可能由非最佳模型引起的潜在错误的来源。然而，也发现 DNA 的结构和动力学特性（作为带电荷大分子的一个例子）在近生理条件下相当独立于所使用的离子模型，为大多数已经发表的大分子模拟提供了支持。
