Skip to main content
SpringerLink
Log in

GridMol: a grid application for molecular modeling and visualization

  • Published:
Journal of Computer-Aided Molecular Design Aims and scope Submit manuscript

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

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12
Fig. 13
Fig. 14
Fig. 15
Fig. 16
Fig. 17
Fig. 18
Fig. 19

Similar content being viewed by others

References

  1. Sayle RA, Milner-White EJ (1995) RASMOL: biomolecular graphics for all. Trends Biochem Sci 20:374–376

    Article  CAS  Google Scholar 

  2. Humphrey W, Dalke A, Schulten K (1996) VMD—visual molecular dynamics. J Mol Graphics 14:33–38

    Article  CAS  Google Scholar 

  3. Koradi R, Billeter M, Wüthrich K (1996) MOLMOL: a program for display and analysis of macromolecylar structure. J Mol Graph 14:51–55

    Article  CAS  Google Scholar 

  4. Gaussian. http://www.gaussian.com/ (accessed Oct 2007)

  5. GAMESS. http://www.msg.ameslab.gov/gamess/ (accessed Oct 2007)

  6. GROMACS. http://www.gromacs.org/ (accessed Oct 2007)

  7. CSE-online. http://cse-online.net/ (accessed Oct 2007)

  8. GridChem http://Grid-devel.sdsc.edu/gemstone (accessed Oct 2007)

  9. Reality Grid. http://www.realitygrid.org/ (accessed Oct 2007)

  10. GEMSTONE. http://Grid-devel.sdsc.edu/gemstone (accessed Oct 2007)

  11. JMV—Java Molecular Viewer http://www.ks.uiuc.edu/Research/jmv/ (accessed Oct 2007)

  12. Kabsh W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637

    Article  Google Scholar 

  13. Catmull-room Spline. http://www.mvps.org/directx/articles/catmull/ (accessed Oct 2007)

  14. JMVS. http://www.adcworks.com/projects/jmvs/ (accessed Oct 2007)

  15. Walther D (1997) WebMol—a java based PDB viewer. Trends Biochem Sci 22:274–275. http://www.embl-heidelberg.de/cgi/viewer.pl

    Google Scholar 

  16. Can T, Wang Y, Wang Y-F, Su J (2003) FPV: fast protein visualization using Java 3D™. Bioinformatics 19:913–933

    Article  CAS  Google Scholar 

  17. RCSB protein data bank. http://www.rcsb.org/ (accessed Oct 2007)

  18. 1F8V. http://ndbserver.rutgers.edu/ftp/NDB/coordinates/na-biol-mirror/1f8v.pdb1 (accessed Oct 2007)

  19. China National Grid. http://www.cngrid.org/web/english/home/ (accessed Oct 2007)

Download references

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.

Author information

Authors and Affiliations

  1. Super Computing Center, Computer Network Information Center, Chinese Academy of Sciences, Beijing, 100080, China

    Yanhua Sun, Bin Shen, Zhonghua Lu, Zhong Jin & Xuebin Chi

Authors
  1. Yanhua Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Bin Shen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zhonghua Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zhong Jin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xuebin Chi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Yanhua Sun or Xuebin Chi.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sun, Y., Shen, B., Lu, Z. et al. GridMol: a grid application for molecular modeling and visualization. J Comput Aided Mol Des 22, 119–129 (2008). https://doi.org/10.1007/s10822-008-9183-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10822-008-9183-x

Keywords

Search

Navigation