Free energy calculations from adaptive molecular dynamics simulations with adiabatic reweighting
Free energy calculations from adaptive molecular dynamics simulations with adiabatic reweighting
复制标题
DOI：
10.1063/1.4866811
复制
发表时间：
2014-03-14
影响因子：
4.4
通讯作者：
Athenes, Manuel
中科院分区：
文献类型：
--
作者：
Cao, Lingling;Stoltz, Gabriel;Athenes, Manuel
我们提出了一种绝热加权算法，用于从自适应分子动力学模拟中沿外部参数计算自由能。使用贝叶斯恒等式和来自所有采样配置的信息来估计自适应偏差。我们将该算法应用于团簇中的结构转变和晶体缺陷沿反应坐标的迁移。与标准的自适应分子动力学相比，我们观察到收敛的加速。借助于该算法，还可以沿着反应坐标迭代地构造自由能，而不必微分反应坐标的梯度或任何偏置势。(C)2014 AIP出版有限责任公司。
We propose an adiabatic reweighting algorithm for computing the free energy along an external parameter from adaptive molecular dynamics simulations. The adaptive bias is estimated using Bayes identity and information from all the sampled configurations. We apply the algorithm to a structural transition in a cluster and to the migration of a crystalline defect along a reaction coordinate. Compared to standard adaptive molecular dynamics, we observe an acceleration of convergence. With the aid of the algorithm, it is also possible to iteratively construct the free energy along the reaction coordinate without having to differentiate the gradient of the reaction coordinate or any biasing potential. (C) 2014 AIP Publishing LLC.