.png){kind=icon}
返回
Accelerating molecular modeling applications with graphics processors
.png){kind=icon}
OA
AI
DOI：10.1002/jcc.20829.png)
.png){kind=icon}
.png){kind=icon}
分享.png){kind=icon}
收藏
摘要
En 中文
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.
Keyword:
GPU computing
CUDA
parallel computing
molecular modeling
electrostatic potential
multilevel summation
molecular dynamics
ion placement
multithreading
graphics processing unit
AI总结
对已上传原文的论文进行重点信息的提取，主要内容包括：简要概述、研究摘要、背景介绍、关键亮点、图文解析、展望与总结。
期刊
IF:
4.8
论文数:
7.1K
被引数:
6.1W
机构
暂无机构信息
引用论文
分享收藏
Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent
PREAI
分享收藏Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex环E/螺旋IV rRNA-L25蛋白复合物的长期水合作用，阳离子结合和动力学.png)
BIOPHYSICAL JOURNALOAAI
BIOPHYSICAL JOURNALIF3.1
OAAI分享收藏
查看更多内容