Accelerating molecular modeling applications with graphics processors
Accelerating molecular modeling applications with graphics processors
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DOI：
10.1002/jcc.20829
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发表时间：
2007-12-01
影响因子：
3
通讯作者：
Schulten, Klaus
中科院分区：
文献类型：
--
作者：
Stone, John E.;Phillips, James C.;Schulten, Klaus
分子力学模拟提供了一种在原子细节上研究生物分子行为的计算方法，但这种模拟在规模和时间尺度上受到可用计算资源的限制。最先进的图形处理单元（GPU）每秒可以执行超过5000亿次算术运算，这是一种巨大的计算资源，由于GPU硬件和软件架构的最新进展，现在可以用于通用计算。在这篇文章中，概述了可编程GPU的最新进展，重点是它们在分子力学模拟中的应用，以及在这些情况下获得最佳性能所需的编程技术。我们演示了使用GPU计算分子动力学模拟的远程静电和非键合力，其中基于GPU的计算通常比基于CPU的实现快10-100倍。GPU加速的生物分子模拟的应用程序也证明通过使用GPU加速库仑离子的位置和计算的时间平均电位从分子动力学轨迹。介绍了一种新的库仑势近似计算方法--多级求和法，并与直接库仑求和法进行了比较。根据这组计算获得的性能，未来的应用程序的图形处理器的分子动力学模拟进行了讨论。(c)2007 Wiley Periodicals，Inc.
Molecular mechanics simulations offer a computational approach to study the behavior of biomolecules at atomic detail, but such simulations are limited in size and timescale by the available computing resources. State-of-the-art graphics processing units (GPUs) can perform over 500 billion arithmetic operations per second, a tremendous computational resource that can now be utilized for general purpose computing as a result of recent advances in GPU hardware and software architecture. In this article, an overview of recent advances in programmable GPUs is presented, with an emphasis on their application to molecular mechanics simulations and the programming techniques required to obtain optimal performance in these cases. We demonstrate the use of GPUs for the calculation of long-range electrostatics and nonbonded forces for molecular dynamics simulations, where GPU-based calculations are typically 10-100 times faster than heavily optimized CPU-based implementations. The application of GPU acceleration to biomolecular simulation is also demonstrated through the use of GPU-accelerated Coulomb-based ion placement and calculation of time-averaged potentials from molecular dynamics trajectories. A novel approximation to Coulomb potential calculation, the multilevel summation method, is introduced and compared with direct Coulomb summation. In light of the performance obtained for this set of calculations, future applications of graphics processors to molecular dynamics simulations are discussed. (c) 2007 Wiley Periodicals, Inc.