Multiscale enhanced sampling driven by multiple coarse-grained models
Multiscale enhanced sampling driven by multiple coarse-grained models
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DOI：
10.1016/j.cplett.2014.10.009
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发表时间：
2014-11-25
影响因子：
2.8
通讯作者：
Kidera, Akinori
中科院分区：
文献类型：
--
作者：
Moritsugu, Kei;Terada, Tohru;Kidera, Akinori
增强的采样增加了其在模拟大规模蛋白质功能动力学的重要性。“多尺度增强采样（MSES）”是一种适用于大型蛋白质系统的增强采样方法，其中全原子（MM）采样通过与粗粒度（CG）模型的加速动力学耦合而扩展。在这里，我们表明，MSES的采样效率可以进一步提高使用多个CG副本，而不是一个单一的CG模型，并通过引入CG副本之间的排斥力。应用于明确的溶剂中的chignolin折叠已证明了显着提高采样效率，由于扩展。(C)2014爱思唯尔有限公司版权所有。
Enhanced sampling has increased its importance in simulations of large-scale functional dynamics of proteins. "Multiscale enhanced sampling (MSES)" is an enhanced sampling method applicable to large protein systems, in which all-atom (MM) sampling is extended through a coupling with the accelerated dynamics of a coarse-grained (CG) model. Here, we show that the sampling efficiency of MSES can be further improved by using multiple CG copies instead of a single CG model and by introducing repulsive forces between the CG copies. An application to chignolin folding in explicit solvent has demonstrated a significant improvement in sampling efficiency due to the extension. (C) 2014 Elsevier B.V. All rights reserved.