A super-linear minimization scheme for the nudged elastic band method
A super-linear minimization scheme for the nudged elastic band method
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DOI：
10.1063/1.1627754
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发表时间：
2003-12-22
影响因子：
4.4
通讯作者：
Brooks, BR
中科院分区：
文献类型：
--
作者：
Chu, JW;Trout, BL;Brooks, BR
在这篇文章中，我们提出了一个超线性最小化方案的轻推弹性带（NEB）的方法，它确定了最小能量路径（MEP）的反应，通过连接中间“复制品”之间的反应物和产品。最小化方案是基于拟牛顿法：所采用的基础牛顿-拉夫森（ABNR）最小化方案。在ABNR最小化的每个步骤中，在用户定义维度的子空间中执行Newton-Raphson过程。在新的Newton-Raphson步长下，路径的切线方向在子空间中自洽地确定。所提出的计划的加速淬火分子动力学最小化，目前的做法，最大限度地减少使用NEB的路径，证明在三个非平凡的测试情况下：异构化的丙氨酸二肽，α-螺旋π-螺旋过渡的丙氨酸十肽，和氧化的二甲基硫醚。还添加了新功能，以便可以在具有灵活加权选项的均方根（RMS）最佳拟合空间中定义副本之间的距离。这提供了一种在具有有限数量的复制品的过程中结合移动的溶剂的效果的方法。从不同的初始结构得到的MEP可以用来研究不同的反应机理，最小化路径的加速增强了NEB方法的适用性。NEB力投影程序的组合，在RMS最佳拟合空间中的灵活的距离定义与任意加权选项，和超线性最小化方案提供了一个框架，以帮助研究生物分子的过渡过程，如蛋白质。(C)2003年，美国物理学会。
In this article, we present a superlinear minimization scheme for the nudged elastic band (NEB) method, which determines a minimum-energy path (MEP) of a reaction via connecting intermediate "replicas'' between the reactant and the product. The minimization scheme is based on a quasi-Newton method: the adopted basis Newton-Raphson (ABNR) minimization scheme. In each step of ABNR minimization, the Newton-Raphson procedure is performed in a subspace of a user-defined dimension. The tangent directions of the path at a new Newton-Raphson step are determined self-consistently in the subspace. The acceleration of the proposed scheme over the quenched molecular-dynamic minimization, the current practice for minimizing a path using NEB, is demonstrated in three nontrivial test cases: isomerization of an alanine dipeptide, alpha-helix to pi-helix transition of an alanine decapeptide, and oxidation of dimethyl sulfide. New features are also added such that the distances between replicas can be defined in the root of mean squared (RMS) best-fit space with flexible weighting options. This offers a way to incorporate the effects of a mobile solvent in the process with a finite number of replicas. MEPs obtained from various initial structures can be used to investigate different proposed reaction mechanisms, and the speedup of minimizing a path enhances the applicability of the NEB method. The combination of NEB force projection procedures, the flexible distance definition in the RMS best fit space with arbitrary weighting options, and the superlinear minimization scheme provides a framework to aid in the study of transition processes of biological molecules as such proteins. (C) 2003 American Institute of Physics.