Adaptive Lambda Square Dynamics Simulation: An Efficient Conformational Sampling Method for Biomolecules
Adaptive Lambda Square Dynamics Simulation: An Efficient Conformational Sampling Method for Biomolecules
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DOI：
10.1002/jcc.23462
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发表时间：
2014-01-05
影响因子：
3
通讯作者：
Kono, Hidetoshi
中科院分区：
文献类型：
--
作者：
Ikebe, Jinzen;Sakuraba, Shun;Kono, Hidetoshi
提出了一种新的、高效的生物分子采样方法。部分多电子分子动力学（McMD）是最近发展起来的一种方法，它改进了广义系综（GE）方法，将采样只集中在系统的一部分（GEPS）上；然而，它没有得到很好的测试。我们发现，部分McMD对聚赖氨酸十肽的取样效果不佳，取样效率明显低于常规GE。在此，我们阐明了这一问题的根本原因，并提出了一种新的GEPS，即自适应lambda平方动力学（ALSD），它可以解决使用部分McMD时面临的问题。我们证明，与传统的GE相比，ALSD大大提高了采样效率。我们认为ALSD是一种有效的方法，适用于更大更复杂的生物分子系统的构象采样。(c) 2013 Wiley Periodicals, Inc.；
A novel, efficient sampling method for biomolecules is proposed. The partial multicanonical molecular dynamics (McMD) was recently developed as a method that improved generalized ensemble (GE) methods to focus sampling only on a part of a system (GEPS); however, it was not tested well. We found that partial McMD did not work well for polylysine decapeptide and gave significantly worse sampling efficiency than a conventional GE. Herein, we elucidate the fundamental reason for this and propose a novel GEPS, adaptive lambda square dynamics (ALSD), which can resolve the problem faced when using partial McMD. We demonstrate that ALSD greatly increases the sampling efficiency over a conventional GE. We believe that ALSD is an effective method and is applicable to the conformational sampling of larger and more complicated biomolecule systems. (c) 2013 Wiley Periodicals, Inc.