GISMOS: Graphics and Interactive Steering of MOlecular Simulations

  • Calle Lejdfors
  • Malek O. Khan
  • Anders Ynnerman
  • Bo Jönsson
Conference paper
Part of the Lecture Notes in Computational Science and Engineering book series (LNCSE, volume 13)

Abstract

A modular software package for computational steering and visualization of molecular simulations is presented. The package, GISMOS, builds on instrumentation of existing Fortran programs to accomplish data extraction for visualization as well as run time input of control parameters for steering. A set of template files for instrumentation is provided to minimize the effort required by programmers to attach GISMOS to existing codes. Standard libraries and procedures for user interfaces, graphics production, and inter-process communication are used to ensure flexibility and portability of the package. The interactive steering environment contains a GUI for static and dynamic properties of the simulation as well as tools for 2D and 3D visualization. A Monte Carlo simulation code has been used as a case study. The implementation clearly shows the potential value of GISMOS in research and education. In addition, GISMOS has proven to be a powerful tool for debugging purposes.

Keywords

Coord Agram 

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References

  1. 1.
    M. P. Allen and D. J. Tildesley. Computer Simulation of Liquids. Oxford University Press, Oxford, England, 1989. Paperback.Google Scholar
  2. 2.
    G. A. Geist II, J. A. Kohl, and P. M. Papadopoulos. Cumulvs: Providing fault tolerance, visualization, and steering of parallel applications. Int. J. Supercomputer Applications and High Performance Comp., 11, 1997.Google Scholar
  3. 3.
    G. Hanyzewski and M. Mull. Hermes: A tool kit for developing distributed modelling applications. Nanotechnology, 7, 1996.Google Scholar
  4. 4.
    W. F. Humphrey, A. Dalke, and K. Schulten. VMD: Visual molecular dynamics J. Mol. Graphics, 14, 1996.Google Scholar
  5. 5.
    M. O. Khan and B. Jönsson. Electrostatic correlations fold DNA. Biopolymers, 49, 1999.Google Scholar
  6. 6.
    J. Leech, J. F. Prins, and J. Hermans. SMD: Visual steering of molecular dynamics for protein design. IEEE Comp. Sci. Eng., 3, 1996.Google Scholar
  7. 7.
    Lund University, Division of Structural Mechanics, Lund, Sweden. Interactive Visualization Framework Ivf++: User’s Guide. Under development.Google Scholar
  8. 8.
    B. H. McCormick, T. A. Defanti, and M. D. Brown. Visualization in scientific computing. Computer Graphics, 22, 1987.Google Scholar
  9. 9.
    S. Mel’nikov, M. O. Khan, B. Lindman, and B. Jönsson. Phase behaviour of single DNA in mixed solvents. J. Am. Chem. Soc., 121, 1999.Google Scholar
  10. 10.
    J. D. Mulder, J. J. van Wijk, and R. van Liere. A survey of computational steering environments. FGCS, 15, 1999.Google Scholar
  11. 11.
    S. G. Parker, C. R. Johnson, and D. Beazley. Computational steering software systems and strategies. IEEE Comp. Sci. Eng., 4, 1997.Google Scholar
  12. 12.
    J. F. Prins, J. Hermans, G. Mann, L. S. Nyland, and M. Simons. A virtual environment for steered molecular dynamics FGCS, 15, 1999.Google Scholar
  13. 13.
    R. van Liere, J. D. Mulder, and J. J. van Wijk. Computational steering. FGCS, 12, 1997.Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2000

Authors and Affiliations

  • Calle Lejdfors
    • 1
  • Malek O. Khan
    • 1
  • Anders Ynnerman
    • 2
  • Bo Jönsson
    • 1
  1. 1.Theoretical Chemistry, Chemical CenterLund UniversityLundSweden
  2. 2.National Supercomputer CenterLinköping UniversityLinköpingSweden

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