Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: A general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations
Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: A general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations
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DOI：
10.1063/1.2424700
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发表时间：
2007-01-14
影响因子：
4.4
通讯作者：
Yang, Wei
中科院分区：
文献类型：
--
作者：
Li, Hongzhi;Fajer, Mikolai;Yang, Wei
一个潜在的缩放版本的模拟回火有效地采样配置空间中的局部区域。目前的“模拟缩放”方法是开发与Wang-Landau类型的更新计划，以迅速平坦的缩放参数lambda（m）空间中的分布。这一建议对于需要局部取样的广泛的生物物理问题是有意义的。除了其在局部构象采样中的上级能力和鲁棒性之外，当应用双拓扑炼金术混合势时，这种模拟缩放方法也可以自然地导致有效的“炼金术”自由能预测;从而同时，两个端点化学状态的化学和构象上不同的部分都可以被有效地采样。如在这项工作中所示，本方法也是可行的量子力学和量子力学/分子力学模拟。(c)2007年，美国物理学会。
A potential scaling version of simulated tempering is presented to efficiently sample configuration space in a localized region. The present "simulated scaling" method is developed with a Wang-Landau type of updating scheme in order to quickly flatten the distributions in the scaling parameter lambda(m) space. This proposal is meaningful for a broad range of biophysical problems, in which localized sampling is required. Besides its superior capability and robustness in localized conformational sampling, this simulated scaling method can also naturally lead to efficient "alchemical" free energy predictions when dual-topology alchemical hybrid potential is applied; thereby simultaneously, both of the chemically and conformationally distinct portions of two end point chemical states can be efficiently sampled. As demonstrated in this work, the present method is also feasible for the quantum mechanical and quantum mechanical/molecular mechanical simulations. (c) 2007 American Institute of Physics.