The adaptive biasing force method: everything you always wanted to know but were afraid to ask.
The adaptive biasing force method: everything you always wanted to know but were afraid to ask.
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DOI：
10.1021/jp506633n
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发表时间：
2015-01-22
期刊：
影响因子：
--
通讯作者：
Chipot C
中科院分区：
文献类型：
--
作者：
Comer J;Gumbart JC;Hénin J;Lelièvre T;Pohorille A;Chipot C
在一系列通过几何变换计算自由能差的数值方案中，自适应偏向力算法已经成为绘制复杂自由能地貌的一条很有前途的路线。它依赖于一个简单的概念，即随着模拟的进行，不断更新的偏向力被添加到运动方程中，使得在长时间限制中，它产生的哈密顿量没有沿感兴趣的过渡坐标作用的平均力。这意味着采样在平坦的自由能表面上均匀进行，从而提供可靠的自由能估计。该算法对实践者的吸引力很大程度上在于它物理上直观的基本思想，以及对自由能景观的先验知识没有任何要求。自2001年成立以来，自适应偏向力方案一直是相当受关注的主题，从对收敛性质的深入数学分析到新的发展和扩展。该方法还成功地应用于许多具有挑战性的化学和生物问题。在这篇贡献中，该方法以一种全面、独立的方式提出，以批判性的眼光讨论其特性、适用性和固有限制，并引入新的扩展。通过对典型分子体系的自由能计算，研究了许多方法学方面的问题，从分层策略到克服正交空间中所谓的隐藏障碍，不仅与自适应偏向力算法有关，而且与其他重要抽样方案有关。在本文讨论的基础上，提出了一些提高计算自由能差的效率和可靠性的良好做法。
In the host of numerical schemes devised to calculate free energy differences by way of geometric transformations, the adaptive biasing force algorithm has emerged as a promising route to map complex free-energy landscapes. It relies upon the simple concept that as a simulation progresses, a continuously updated biasing force is added to the equations of motion, such that in the long-time limit it yields a Hamiltonian devoid of an average force acting along the transition coordinate of interest. This means that sampling proceeds uniformly on a flat free-energy surface, thus providing reliable free-energy estimates. Much of the appeal of the algorithm to the practitioner is in its physically intuitive underlying ideas and the absence of any requirements for prior knowledge about free-energy landscapes. Since its inception in 2001, the adaptive biasing force scheme has been the subject of considerable attention, from in-depth mathematical analysis of convergence properties to novel developments and extensions. The method has also been successfully applied to many challenging problems in chemistry and biology. In this contribution, the method is presented in a comprehensive, self-contained fashion, discussing with a critical eye its properties, applicability, and inherent limitations, as well as introducing novel extensions. Through free-energy calculations of prototypical molecular systems, many methodological aspects are examined, from stratification strategies to overcoming the so-called hidden barriers in orthogonal space, relevant not only to the adaptive biasing force algorithm but also to other importance-sampling schemes. On the basis of the discussions in this paper, a number of good practices for improving the efficiency and reliability of the computed free-energy differences are proposed.
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影响因子：
4.4
作者：
Cao, Lingling;Stoltz, Gabriel;Athenes, Manuel
通讯作者：
Athenes, Manuel
影响因子：
4.4
作者：
Chipot, C;Hénin, J
通讯作者：
Hénin, J
DOI：
10.1073/pnas.0408098102
发表时间：
2005-05-10
影响因子：
11.1
作者：
Best, RB;Hummer, G
通讯作者：
Hummer, G
影响因子：
4.4
作者：
Bartels, C;Schaefer, M;Karplus, M
通讯作者：
Karplus, M
影响因子：
2.8
作者：
CARTER, EA;CICCOTTI, G;KAPRAL, R
通讯作者：
KAPRAL, R