Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units.
Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units.
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DOI：
10.1021/ct400514p
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发表时间：
2013-11-12
影响因子：
5.5
通讯作者：
McCammon, J. Andrew
中科院分区：
文献类型：
--
作者：
Lindert, Steffen;Bucher, Denis;Eastman, Peter;Pande, Vijay;McCammon, J. Andrew
加速分子动力学（aMD）方法最近被证明可以提高分子动力学（MD）模拟中生物分子的采样，通常提高几个数量级。在这里，我们描述了OpenMM应用层aMD方法的实现，它充分利用了图形处理单元（gpu）计算的优势。aMD方法与AMOEBA极化力场（AMOEBA-aMD）结合使用，可以模拟具有极化力场的长时间尺度事件。实验结果表明，AMOEBA-aMD方法是有效实现的，其标准参数化结果准确。对于BPTI蛋白，我们证明了用阿米巴描述的蛋白质结构即使在高水平加速度下获得的延长时间尺度上也保持稳定。对于DNA修复金属酶内切酶IV，我们表明使用变形虫力场是对描述酶活性位点的固定带电模型的显着改进。新的AMOEBA-aMD方法是公开可用的（），并且有望成为研究复杂系统的有趣方法，可以从极化力场的使用和增强采样中受益。
The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available () and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling.
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影响因子：
5.5
作者：
Goetz, Andreas W.;Williamson, Mark J.;Xu, Dong;Poole, Duncan;Le Grand, Scott;Walker, Ross C.
通讯作者：
Walker, Ross C.
影响因子：
3.7
作者：
Lindorff-Larsen K;Maragakis P;Piana S;Eastwood MP;Dror RO;Shaw DE
通讯作者：
Shaw DE
影响因子：
64.5
作者：
Hosfield, DJ;Guan, Y;Tainer, JA
通讯作者：
Tainer, JA
影响因子：
3.3
作者：
Baker, Christopher M.;Anisimov, Victor M.;MacKerell, Alexander D., Jr.
通讯作者：
MacKerell, Alexander D., Jr.
影响因子：
4.4
作者：
JORGENSEN, WL;CHANDRASEKHAR, J;KLEIN, ML
通讯作者：
KLEIN, ML