High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD.
High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD.
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DOI：
10.1021/jz101461d
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发表时间：
2011
期刊：
影响因子：
--
通讯作者：
Roux B
中科院分区：
文献类型：
--
作者：
Jiang W;Hardy DJ;Phillips JC;Mackerell AD Jr;Schulten K;Roux B
在大规模原子分子动力学(MD)模拟中加入激发极化的影响是提高计算精度的关键挑战。一种计算上有效的处理方法是基于经典的德鲁德振子，在这种振子中，一个辅助带电粒子通过弹簧连接到每个原子核上。在这里，我们报告了该模型在NAMD程序中的第一个实现。将扩展的拉格朗日动力学和双朗之万恒温格式应用于Drude-核对，在自洽场极限附近有效地产生了经典的动力学传播。在大规模分布的超级计算平台上，基于Drude可极化力场尺度的大规模MD模拟效果很好，计算需求仅比不可极化模型高出约50%-100%。以150 mm的氯化钠水溶液为例进行了模拟，计算的离子电导率与实验符合得很好。
Incorporating the influence of induced polarization in large-scale atomistic molecular dynamics (MD) simulations is a critical challenge in the progress toward computations of increased accuracy. One computationally efficient treatment is based on the classical Drude oscillator in which an auxiliary charged particle is attached by a spring to each nucleus. Here, we report the first implementation of this model in the program NAMD. An extended Lagrangian dynamics with a dual-Langevin thermostat scheme applied to the Drude-nucleus pairs is employed to efficiently generate classical dynamic propagation near the self-consistent field limit. Large-scale MD simulations based on the Drude polarizable force field scale very well on massively distributed supercomputing platforms, the computational demand being only about 50–100% higher than for nonpolarizable models. As an illustration, a large-scale 150 mM NaCl aqueous salt solution is simulated, and the calculated ionic conductivity is shown to be in excellent agreement with experiment.
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