Polarizable force fields for molecular dynamics simulations of biomolecules
Polarizable force fields for molecular dynamics simulations of biomolecules
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DOI：
10.1002/wcms.1215
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发表时间：
2015-03-01
影响因子：
11.4
通讯作者：
Baker, Christopher M.
中科院分区：
文献类型：
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作者：
Baker, Christopher M.
分子动力学模拟已广泛应用于生物分子系统的研究。在这些模拟中，称为力场的能量函数用于确定作用于原子和分子的力。虽然这些力场非常成功，但它们包含许多近似值，包括克服计算能力的限制。这些近似中最重要的一个是省略了极化率，极化率是分子中电荷分布响应其环境而变化的过程。由于已知极化率在许多生化情况下很重要，并且由于计算机硬件的进步减少了对力场内近似的需要，因此人们对使用包括极化率的显式表示的力场产生了很大的兴趣。因此，许多极化力场正在开发中：这些在很大程度上是实验性的，其使用仅限于专业研究人员。这种情况现在正在改变。完全优化的极化力场的参数正在发布，相关代码已纳入标准仿真软件中。百纳秒时间尺度的模拟正在被报道，并且现在所有模拟科学家都可以实现。在本概述中，我研究了可用于模拟生物分子的极化力场、它们所应用的系统，以及极化性可以带来的好处和挑战。在考虑极化力场的未来发展方向时，我研究了从非极化力场中吸取的经验教训，并强调了仍有待解决的问题。 (C) 2015 约翰威利父子公司。
Molecular dynamics simulations are well established for the study of biomolecular systems. Within these simulations, energy functions known as force fields are used to determine the forces acting on atoms and molecules. While these force fields have been very successful, they contain a number of approximations, included to overcome limitations in computing power. One of the most important of these approximations is the omission of polarizability, the process by which the charge distribution in a molecule changes in response to its environment. Since polarizability is known to be important in many biochemical situations, and since advances in computer hardware have reduced the need for approximations within force fields, there is major interest in the use of force fields that include an explicit representation of polarizability. As such, a number of polarizable force fields have been under development: these have been largely experimental, and their use restricted to specialized researchers. This situation is now changing. Parameters for fully optimized polarizable force fields are being published, and associated code incorporated into standard simulation software. Simulations on the hundred-nanosecond timescale are being reported, and are now within reach of all simulation scientists. In this overview, I examine the polarizable force fields available for the simulation of biomolecules, the systems to which they have been applied, and the benefits and challenges that polarizability can bring. In considering future directions for development of polarizable force fields, I examine lessons learnt from non-polarizable force fields, and highlight issues that remain to be addressed. (C) 2015 John Wiley & Sons, Ltd.