EGO: A Parallel Program for Molecular Dynamics Simulations of Biomolecules

Markus Eichinger, Helmut Grubmüller, and Helmut Heller

Support: MPIbpc, DFG (GR 1590/1-2), EU (BIO4-CT98-0024), VW Foundation, LRZ

About the MD program EGO_VIII

EGO manual

Download EGO source code

Download EGO manual (PostScript)

Download EGO manual (PostScript, gnu-zipped)

Download EGO manual (PDF)

References to the developers of EGO_VIII

Development of a first version of EGO by Helmut Heller and Helmut Grubmüller was initiated by Klaus Schulten in his group at the Technical University of Munich. Development continued at the University of Illinois at Urbana-Champaign, IL, U.S.A., and, subsequently, in the group of Paul Tavan at the University of Munich. There, EGO was completely rewritten mainly by Markus Eichinger. Today, program development continues at the theoretical molecular biophysics group of Helmut Grubmüller at the Max-Planck-Institute for biophysical chemistry, Göttingen, at the University of Munich, as well as at the High Performance Computing Group, Leibniz Computer Center, Munich, by Helmut Heller.

If you use the EGO program system for your work, you are kindly requested to cite the following two references:

Furthermore, it would be nice (but is not required) if you dropped us a note (by email), telling us a bit about your application of EGO.

References

  1. Markus Eichinger, Helmut Heller, and Helmut Grubmüller
    EGO - An efficient molecular dynamics program and its application to protein dynamics simulations In Rüdiger Esser, Peter Grassberger, Johannes Grotendorst, and Marius Lewerenz, editors, Workshop on Molecular Dynamics on Parallel Computers, p. 154-174, Singapore 912805, World Scientific, 2000
    A gzip-ed PostScript-version of the paper is available.
  2. Helmut Grubmüller and Paul Tavan
    Multiple Time Step Algorithms for Molecular Dynamics Simulations of Proteins: How Good are they?
    J. Comp. Chem., 19,1534-1552, 1998.
  3. Markus Eichinger, Berthold Heymann, Helmut Heller, Helmut Grubmüller, and Paul Tavan.
    Conformational dynamics simulations of proteins.
    In P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Mark, S. Reich, and R. D. Skeel, editors, Lecture Notes in Computational Science and Engineering Vol 4:Computational Molecular Dynamics: Challenges, Methods, Ideas, p.78-97. Springer, 1998.
    An HTML-version and a gzip-ed PostScript-version of the paper is available.
  4. Markus Eichinger, Helmut Grubmüller, Helmut Heller, and Paul Tavan
    FAMUSAMM: An Algorithm for Rapid Evaluation of Electrostatic Interactions in Molecular Dynamics Simulations
    J. Comp. Chem., 18,1729-1749, 1997. (download)
  5. Christoph Niedermeier and Paul Tavan
    Fast version of the structure adapted multipole method - Efficient calculation of electrostatic forces in protein dynamics
    Molecular Simulation    , 17,57-66, 1996.
  6. Thomas C. Bishop, Helmut Heller, and Klaus Schulten
    Molecular Dynamics on Parallel Computers: Applications for Theoretical Biophysics
    in Rajiv K. Kalia and Priya Vashishta (Eds.): Toward Teraflop Computing and New Grand Challenge Applications,Nova Science Publishers, Inc., New York, p.129-138, 1995.
  7. Markus Eichinger
    Paralleler schneller Multipolalgorithmus mit Mehrschrittverfahren für Molekulardynamiksimulationen
    Diplomarbeit, Technische Universität München, April 1995. (download)
  8. Helmut Grubmüller
    Predicting slow structural transitions in macromolecular systems: conformational flooding
    Phys. Rev. E 52,2893, 1995.
  9. Christoph Niedermeier and Paul Tavan
    A structure adapted multipole method for electrostatic interactions in protein dynamics
    J. Chem. Phys., 101,734-748, 1994.
  10. Amitabh B. Sinha, Klaus Schulten, and Helmut Heller.
    Performance analysis of a parallel molecular dynamics program.
    Comput. Phys. Commun., 78:265-278, 1994. (download)
  11. Helmut Grubmüller
    Molekulardynamik von Proteinen auf langen Zeitskalen
    PhD thesis, Technical University of Munich, Germany, Jan. 1994.
  12. Helmut Heller
    Simulation einer Lipidmembran auf einem Parallelrechner.
    PhD thesis, Technical University of Munich, Germany, December 1993. (download)
  13. Helmut Heller, Michael Schaefer, and Klaus Schulten.
    Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal phases.
    J. Phys. Chem., 97:8343-8360, 1993. (download)
  14. Helmut Grubmüller, Helmut Heller, Andreas Windemuth, and Klaus Schulten
    Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions
    Molecular Simulation, 6,121-142, 1991. ( download)
  15. Helmut Heller, Helmut Grubmüller, and Klaus Schulten
    Molecular Dynamics Simulation on a Parallel Computer
    Molecular Simulation, 5,133-165, 1990. (download)
  16. Helmut Grubmüller
    Dynamiksimulation sehr großer Makromoleküle auf einem Parallelrechner
    Diplomarbeit, Technische Universität München, 1989.
  17. Helmut Heller
    Dynamiksimulation sehr großer Makromoleküle am Beispiel des photosynthetischen Reaktionszentrums von Rhodopseudomonas viridis
    Diplomarbeit, Technische Universität München, 1988. (download)
  18. Helmut Grubmüller, Helmut Heller, and Klaus Schulten.
    Eine Cray für ``jedermann''.
    mc, 11:48-64, 1988. (download).

Helmut Heller / heller@lrz.de