在图形处理单元上加速分子动力学模拟
Accelerating molecular dynamic simulation on graphics processing units.
作者信息
Friedrichs Mark S, Eastman Peter, Vaidyanathan Vishal, Houston Mike, Legrand Scott, Beberg Adam L, Ensign Daniel L, Bruns Christopher M, Pande Vijay S
机构信息
Department of Bioengineering, Stanford University, Stanford, California 94305, USA.
出版信息
J Comput Chem. 2009 Apr 30;30(6):864-72. doi: 10.1002/jcc.21209.
Abstract
We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core.
摘要
我们描述了一种完全在图形处理单元（GPU）上运行的全原子蛋白质分子动力学的完整实现，包括所有标准力场项、积分、约束和隐式溶剂。我们讨论了算法的设计以及充分利用GPU所需的重要优化。我们评估了其性能，并表明它比在单个CPU核心上运行的传统实现快700倍以上。
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