确定活化过程途径和自由能的约束方法
Constraint methods for determining pathways and free energy of activated processes
摘要：
从化学反应到大生物分子的构象转变的活化过程受到障碍的阻碍，这些障碍只能通过输入一些活化自由能来克服。因此，通常的模拟技术的特征和速率确定的势垒区域不充分采样。对反应坐标r的约束已被证明是在不改变势能函数、能量或温度的情况下探索困难途径的合适手段。对于r值的密集序列，相应的模拟序列为该过程提供了路径。由于在每次模拟过程中，数千个坐标中只有一个是固定的，因此路径基本上反映了系统的内部动态。从平均力的自由能分布可以计算得到反应速率和洞察力的反应机理。在过去的十年中，理论工具和计算能力已经发展到一定程度，模拟在定量与实验一致的过程中提供了令人印象深刻的定性见解。在这里，我们介绍了反应途径和坐标，并发展了自由能作为平均力势的理论。阐明了平均力与中心量约束力之间的关系，讨论了质量度规张量修正。良好的表现没有张量校正的坐标被认为是。本文以目标分子动力学模拟的反应坐标为例，讨论了目标分子动力学模拟的理论背景和具体实现。最后，我们比较应用的约束方法和其他技术开发的相同的目的，并讨论了该方法的局限性。
英文摘要：
Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and rate-determining barrier regions are not sufficiently sampled by usual simulation techniques. Constraints on a reaction coordinate r have turned out to be a suitable means to explore difficult pathways without changing potential function, energy or temperature. For a dense sequence of values of r, the corresponding sequence of simulations provides a pathway for the process. As only one coordinate among thousands is fixed during each simulation, the pathway essentially reflects the system's internal dynamics. From mean forces the free energy profile can be calculated to obtain reaction rates and insight in the reaction mechanism. In the last decade, theoretical tools and computing capacity have been developed to a degree where simulations give impressive qualitative insight in the processes at quantitative agreement with experiments. Here, we give an introduction to reaction pathways and coordinates, and develop the theory of free energy as the potential of mean force. We clarify the connection between mean force and constraint force which is the central quantity evaluated, and discuss the mass metric tensor correction. Well-behaved coordinates without tensor correction are considered. We discuss the theoretical background and practical implementation on the example of the reaction coordinate of targeted molecular dynamics simulation. Finally, we compare applications of constraint methods and other techniques developed for the same purpose, and discuss the limits of the approach.
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