Molecular dynamics simulation of macromolecules using graphics processing unit
文献类型：期刊论文
| 作者 | Xu, Ji1,2; Ren, Ying1; Ge, Wei1; Yu, Xiang2,3; Yang, Xiaozhen3; Li, Jinghai1 |
| 刊名 | MOLECULAR SIMULATION
 |
| 出版日期 | 2010 |
| 卷号 | 36期号:14页码:1131-1140 |
| 关键词 | macromolecule molecular dynamics speedup GPU CUDA |
| ISSN号 | 0892-7022 |
| 通讯作者 | Ge, W |
| 英文摘要 | Molecular dynamics (MD) simulation is a powerful computational tool to study the behaviour of macromolecular systems. However, many simulations in this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing units (GPUs) have provided unprecedented computational power for scientific applications. Many MD algorithms suit the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU are presented. For validation, we have performed MD simulations of polymer crystallisation with our GPU package, GPU_MD-1.0.5, and the results agree perfectly with computations on CPUs, meanwhile GPU_MD-1.0.5 achieves about 39 times speedup compared with GROMACS-4.0.5 on a single CPU core. Therefore, our single GPU code has already provided an inexpensive alternative for macromolecular simulations of traditional CPU clusters and will serve as a basis for developing parallel GPU programs to further speed up the computations. |
| WOS标题词 | Science & Technology ; Physical Sciences |
| 类目[WOS] | Chemistry, Physical ; Physics, Atomic, Molecular & Chemical |
| 研究领域[WOS] | Chemistry ; Physics |
| 关键词[WOS] | CANONICAL ENSEMBLE ; CRYSTALLIZATION ; ALGORITHMS ; GROMACS |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000285199400003 |
| 公开日期 | 2013-11-28 |
| 版本 | 出版稿 |
| 源URL | [http://ir.ipe.ac.cn/handle/122111/6253]  |
| 专题 | 过程工程研究所_多相复杂系统国家重点实验室 |
| 作者单位 | 1.Chinese Acad Sci, Inst Proc Engn, State Key Lab Multiphase Complex Syst, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Grad Univ, Beijing 100039, Peoples R China 3.Chinese Acad Sci, Inst Chem, Joint Lab Polymer Sci & Mat, Beijing Natl Lab Mol Sci, Beijing 100190, Peoples R China |
| 推荐引用方式 GB/T 7714 | Xu, Ji,Ren, Ying,Ge, Wei,et al. Molecular dynamics simulation of macromolecules using graphics processing unit[J]. MOLECULAR SIMULATION,2010,36(14):1131-1140. |
| APA | Xu, Ji,Ren, Ying,Ge, Wei,Yu, Xiang,Yang, Xiaozhen,&Li, Jinghai.(2010).Molecular dynamics simulation of macromolecules using graphics processing unit.MOLECULAR SIMULATION,36(14),1131-1140. |
| MLA | Xu, Ji,et al."Molecular dynamics simulation of macromolecules using graphics processing unit".MOLECULAR SIMULATION 36.14(2010):1131-1140. |
入库方式： OAI收割
来源：过程工程研究所
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