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Molecular dynamics simulation of macromolecules using graphics processing unit
Xu, Ji1,2; Ren, Ying1; Ge, Wei1; Yu, Xiang2,3; Yang, Xiaozhen3; Li, Jinghai1; Ge, W
2010
Source PublicationMOLECULAR SIMULATION
ISSN0892-7022
Volume36Issue:14Pages:1131-1140
AbstractMolecular 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.
KeywordMacromolecule Molecular Dynamics Speedup Gpu Cuda
SubtypeArticle
WOS HeadingsScience & Technology ; Physical Sciences
DOI10.1080/08927022.2010.506512
Indexed BySCI
Language英语
WOS KeywordCANONICAL ENSEMBLE ; CRYSTALLIZATION ; ALGORITHMS ; GROMACS
WOS Research AreaChemistry ; Physics
WOS SubjectChemistry, Physical ; Physics, Atomic, Molecular & Chemical
WOS IDWOS:000285199400003
Citation statistics
Cited Times:15[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Version出版稿
Identifierhttp://ir.ipe.ac.cn/handle/122111/6253
Collection多相复杂系统国家重点实验室
Corresponding AuthorGe, W
Affiliation1.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
Recommended Citation
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.,...&Ge, W.(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.
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