Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
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DOI：
10.1021/ct400314y
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发表时间：
2013-09-01
影响因子：
5.5
通讯作者：
Walker, Ross C.
中科院分区：
文献类型：
--
作者：
Salomon-Ferrer, Romelia;Goetz, Andreas W.;Walker, Ross C.
我们介绍了完全在启用CUDA的GPU上运行的Amber程序软件包中明确的所有原子经典分子动力学（MD）的实现。该实现在2010年4月首次公开发行，作为Amber MD软件包版本11的一部分，并在过去两年中进一步改进和优化，该实施支持了三种最广泛使用的统计机械合奏（NVE，NVT和NPT），它使用了粒子网格Ewald（PME）用于远程静电，并完全在支持CUDA的NVIDIA图形处理单元（GPU）上运行，提供结果从统计学上讲，与该软件的传统CPU版本没有区别，并且性能超过了CPU版本的Amber软件在所有基于CPU的所有基于CPU的群集和超级计算机上都可实现的。我们简要讨论了专门为这项工作开发的三个不同的精度模型（SPDP，SPFP和DPDP），并突出了该方法的技术细节，因为该方法扩展到了先前报道的工作[Gotz等，J。Chem。理论计算。 2012，doi：10.1021/ct200909j; Le Grand等人，Comp。物理。通讯。 2013，doi：10.1016/j.cpc.2012.09.022]。我们强调了在传统CPU的机器上看到的性能的实质性改进，并提供了我们的实施和精确模型的验证。我们还提供了支持我们决定从琥珀软件包的最新版本中删除先前描述的完全单个精度（SPSP）模型的决定的证据。
We present an implementation of explicit solvent all atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA-enabled GPUs. First released publicly in April 2010 as part of version 11 of the AMBER MD package and further improved and optimized over the last two years, this implementation supports the three most widely used statistical mechanical ensembles (NVE, NVT, and NPT), uses particle mesh Ewald (PME) for the long-range electrostatics, and runs entirely on CUDA-enabled NVIDIA graphics processing units (GPUs), providing results that are statistically indistinguishable from the traditional CPU version of the software and with performance that exceeds that achievable by the CPU version of AMBER software running on all conventional CPU-based clusters and supercomputers. We briefly discuss three different precision models developed specifically for this work (SPDP, SPFP, and DPDP) and highlight the technical details of the approach as it extends beyond previously reported work [Gotz et al., J. Chem. Theory Comput. 2012, DOI: 10.1021/ct200909j; Le Grand et al., Comp. Phys. Comm. 2013, DOI: 10.1016/j.cpc.2012.09.022]. We highlight the substantial improvements in performance that are seen over traditional CPU-only machines and provide validation of our implementation and precision models. We also provide evidence supporting our decision to deprecate the previously described fully single precision (SPSP) model from the latest release of the AMBER software package.