Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born.
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born.
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DOI：
10.1021/ct200909j
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发表时间：
2012-05-08
影响因子：
5.5
通讯作者：
Walker, Ross C.
中科院分区：
文献类型：
--
作者：
Goetz, Andreas W.;Williamson, Mark J.;Xu, Dong;Poole, Duncan;Le Grand, Scott;Walker, Ross C.
我们提出了一种实现广义玻恩隐式溶剂全原子经典分子动力学（MD）的AMBER程序包，完全运行在CUDA启用NVIDIA图形处理单元（GPU）。我们讨论的算法，用于利用GPU的处理能力，并显示的性能，可以实现在传统的CPU集群上的模拟比较。该实现支持三种不同的精度模型，其中对力的贡献在单精度浮点运算中计算，但在双精度（SPDP）中累积，或者一切都在单精度（SPSP）或双精度（DPDP）中计算。除了性能，我们还专注于理解不同精度模型对隐式溶剂MD模拟结果的影响。我们展示了一系列测试的结果，包括单点力评估的准确性和能量守恒以及与蛋白质动力学相关的结构特性。由于SPSP精度模型内的舍入误差而产生的数值噪声足够大，导致误差累积，这可能导致长时间尺度模拟的非物理轨迹。我们建议使用的混合精度SPDP模型，因为获得的数值结果是可比的全双精度DPDP模型和参考双精度CPU实现，但在显着降低计算成本。我们的实现提供了GB的模拟性能在一个单一的桌面上，相当于，在某些情况下，超过了传统的超级计算机。
We present an implementation of generalized Born implicit solvent all-atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA enabled NVIDIA graphics processing units (GPUs). We discuss the algorithms that are used to exploit the processing power of the GPUs and show the performance that can be achieved in comparison to simulations on conventional CPU clusters. The implementation supports three different precision models in which the contributions to the forces are calculated in single precision floating point arithmetic but accumulated in double precision (SPDP), or everything is computed in single precision (SPSP) or double precision (DPDP). In addition to performance, we have focused on understanding the implications of the different precision models on the outcome of implicit solvent MD simulations. We show results for a range of tests including the accuracy of single point force evaluations and energy conservation as well as structural properties pertainining to protein dynamics. The numerical noise due to rounding errors within the SPSP precision model is sufficiently large to lead to an accumulation of errors which can result in unphysical trajectories for long time scale simulations. We recommend the use of the mixed-precision SPDP model since the numerical results obtained are comparable with those of the full double precision DPDP model and the reference double precision CPU implementation but at significantly reduced computational cost. Our implementation provides performance for GB simulations on a single desktop that is on par with, and in some cases exceeds, that of traditional supercomputers.
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