The adaptive buffered force QM/MM method in the CP2K and AMBER software packages.
The adaptive buffered force QM/MM method in the CP2K and AMBER software packages.
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CP2K 和 AMBER 软件包中的自适应缓冲力 QM/MM 方法。
DOI：
10.1002/jcc.23839
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发表时间：
2015
影响因子：
3
通讯作者：
Mones L
中科院分区：
文献类型：
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作者：
Mones L
本文介绍了自适应缓冲力（AdBF）量子力学/分子力学（QM/MM）方法在CP2K和AMBER两个流行的封装中的实现和验证。实现建立在每个代码中现有的QM/MM功能的基础上，扩展它以允许在模拟期间重新定义QM和MM区域，并通过根据缓冲力混合方法丢弃边界附近的力来减少QM - MM接口错误。还实现了力混合方法所需的新型自适应恒温器。采用各种半经验哈密顿量和密度泛函理论作为QM模型，通过模拟散装水的结构，锌存在下的水自水解和二甲基磷酸水解，对该方法的不同变体进行了基准测试。结果表明，在适当的参数下，基于力收敛试验的AdBF QM/MM方案可以提供与相应的全QM模拟相匹配的动态QM区域结构的精确逼近，并且在所有情况下都能再现正确的能量学。自适应无缓冲力混合和自适应传统QM/MM方法也为某些系统提供了合理的结果，但更容易受到不稳定和不准确的影响。©2015作者。计算化学杂志，Wiley期刊公司出版。
The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM‐MM interface errors by discarding forces near the boundary according to the buffered force‐mixing approach. New adaptive thermostats, needed by force‐mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl‐phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force‐mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.