用于基于 GROMOS 软件的生物分子模拟的 GPU 溶剂-溶剂相互作用计算加速器。
A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software.
机构信息
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, Zürich 8093, Switzerland.
出版信息
J Comput Chem. 2010 Jun;31(8):1636-43. doi: 10.1002/jcc.21447.
During the past few years, graphics processing units (GPUs) have become extremely popular in the high performance computing community. In this study, we present an implementation of an acceleration engine for the solvent-solvent interaction evaluation of molecular dynamics simulations. By careful optimization of the algorithm speed-ups up to a factor of 54 (single-precision GPU vs. double-precision CPU) could be achieved. The accuracy of the single-precision GPU implementation is carefully investigated and does not influence structural, thermodynamic, and dynamic quantities. Therefore, the implementation enables users of the GROMOS software for biomolecular simulation to run the solvent-solvent interaction evaluation on a GPU, and thus, to speed-up their simulations by a factor 6-9.
在过去的几年中，图形处理单元（GPU）在高性能计算领域变得非常流行。在这项研究中，我们提出了一种用于分子动力学模拟溶剂-溶剂相互作用评估的加速引擎的实现。通过对算法进行仔细的优化，我们实现了高达 54 倍的加速（单精度 GPU 与双精度 CPU）。我们仔细研究了单精度 GPU 实现的准确性，它不会影响结构、热力学和动力学参数。因此，该实现使用户能够在 GPU 上运行 GROMOS 软件的溶剂-溶剂相互作用评估，从而将模拟速度提高 6-9 倍。
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