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  • 标题:Performance Analysis Cluster Computing Environments on Molecular Dynamic Simulation of RAD GTPase and LOXCurcumin Molecules with AMBER
  • 本地全文:下载
  • 作者:Heru Suhartanto ; Arry Yanuar ; M. H. Hilman
  • 期刊名称:International Journal of Computer Science Issues
  • 印刷版ISSN:1694-0784
  • 电子版ISSN:1694-0814
  • 出版年度:2012
  • 卷号:9
  • 期号:2
  • 出版社:IJCSI Press
  • 摘要:Implementation of virtual laboratory on scientific research has produced huge acceleration. One of the virtual scientific research activity is molecular dynamic simulation. The virtual experiments need high computing resources to solve the problem. AMBER is one of the software that provides molecular dynamic simulation that can utilize the parallel computing facilities. In this paper, we conduct the molecular dynamic experiments in order to know reliability of cluster computing environment. The results show that an implicit solvent simulation takes longer time than that in vacuum scenario since one has to consider existence of solvent surround the molecules so the computation is much longer than in vacuum; that the speed up will likely to remain constant on certain additional number of processors; and that there is no significant speed up for case in the LOX-Curcumin explicit solvent simulation.
  • 关键词:Performance Analysis; Molecular Dynamic; Cluster Computing; AMBER.
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