Advanced Potential Energy Surfaces for Molecular Simulation.
Advanced Potential Energy Surfaces for Molecular Simulation.
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DOI：
10.1021/acs.jpcb.6b06414
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发表时间：
2016-09-22
影响因子：
3.3
通讯作者：
Head-Gordon, Teresa
中科院分区：
文献类型：
--
作者：
Albaugh, Alex;Boateng, Henry A.;Bradshaw, Richard T.;Demerdash, Omar N.;Dziedzic, Jacek;Mao, Yuezhi;Margul, Daniel T.;Swails, Jason;Zeng, Qiao;Case, David A.;Eastman, Peter;Wang, Lee-Ping;Essex, Jonathan W.;Head-Gordon, Martin;Pande, Vijay S.;Ponder, Jay W.;Shao, Yihan;Skylaris, Chris-Kriton;Todorov, Ilian T.;Tuckerman, Mark E.;Head-Gordon, Teresa
先进的势能面，定义为经典或混合量子经典（QM/MM）处理，超越了广泛使用的经典固定电荷，成对加性力场，在进行凝聚相模拟时遇到了多个软件挑战：理论模型的计算成本，缺乏可以降低成本的近似模型和算法的创新，对广泛的社区代码的传播有限，理论模型之间的软件接口开发不足，HPC架构和更新的GPU和多核硬件上的软件实现质量落后。在这篇专题文章中，我们回顾了这些领域的最新进展，包括定义良好的极化近似和新的多极静电公式，求解互极化方程和增加MD时间步长的新方法，将线性标度电子结构方法与新的QM/MM方法相结合，解释两个区域之间的互极化，以及这些模型和方法在GPU和CPU硬件平台上的大大改进的软件部署。我们现在已经接近了一个时代，多极基极化力场可以常规使用，以获得计算结果相比，国家的最先进的密度泛函理论，同时达到采样统计是可以接受的，当从更简单的固定部分电荷力场。
Advanced potential energy surfaces, defined as classical or mixed quantum-classical (QM/MM) treatments beyond widely available classical fixed-charge, pairwise-additive force fields, have encountered multiple software challenges for conducting condensed phase simulations: computational cost of the theoretical models, lack of innovation in approximate models and algorithms that can mitigate the cost, limited dissemination to a broad range of community codes, under-developed software interfaces between theoretical models, and lagging quality software implementations on HPC architectures and newer GPU and multicore hardware. In this Feature article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.
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DOI：
10.1088/0953-8984/21/33/333102
发表时间：
2009-08-19
期刊：
Journal of physics. Condensed matter : an Institute of Physics journal
影响因子：
--
作者：
Cieplak P;Dupradeau FY;Duan Y;Wang J
通讯作者：
Wang J
影响因子：
4.1
作者：
BENNETT, CH
通讯作者：
BENNETT, CH
DOI：
10.1039/c6cp02509a
发表时间：
2016-11-09
期刊：
Physical chemistry chemical physics : PCCP
影响因子：
--
作者：
Bell DR;Qi R;Jing Z;Xiang JY;Mejias C;Schnieders MJ;Ponder JW;Ren P
通讯作者：
Ren P
DOI：
10.1073/pnas.0502962102
发表时间：
2005-05-31
影响因子：
11.1
作者：
Donchev, AG;Ozrin, VD;Tarasov, VI
通讯作者：
Tarasov, VI
影响因子：
6.3
作者：
Bush, I. J.;Todorov, I. T.;Smith, W.
通讯作者：
Smith, W.