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Journal of Computer-Aided Molecular Design

, Volume 22, Issue 2, pp 119–129 | Cite as

GridMol: a grid application for molecular modeling and visualization

  • Yanhua Sun
  • Bin Shen
  • Zhonghua Lu
  • Zhong Jin
  • Xuebin Chi
Article

Abstract

In this paper we present GridMol, an extensible tool for building a high performance computational chemistry platform in the grid environment. GridMol provides computational chemists one-stop service for molecular modeling, scientific computing and molecular information visualization. GridMol is not only a visualization and modeling tool but also simplifies control of remote Grid software that can access high performance computing resources. GridMol has been successfully integrated into China National Grid, the most powerful Chinese Grid Computing platform. In Section “Grid computing” of this paper, a computing example is given to show the availability and efficiency of GridMol. GridMol is coded using Java and Java3D for portability and cross-platform compatibility (Windows, Linux, MacOS X and UNIX). GridMol can run not only as a stand-alone application, but also as an applet through web browsers. In this paper, we will present the techniques for molecular visualization, molecular modeling and grid computing. GridMol is available free of charge under the GNU Public License (GPL) from our website: http://www.sccas.cn/~syh/GridMol/index.html Contact: syh@sccas.cn

Keywords

Grid computing GridMol Java 3D™ Molecular visualization Molecular modeling One-stop service Protein secondary structure 

Notes

Acknowledgements

We wish to thank Ryan Ferrell for his comments on this paper. This work is funded by The National High Technology Research and Development Program of China (863 Program) from The Ministry of Science and Technology, PRC, under grant 2006AA01A119, National Natural Science Foundation of China under grant 60673064.

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Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  1. 1.Super Computing Center, Computer Network Information CenterChinese Academy of SciencesBeijingChina

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