The Molecular Dynamics program EGO VIII

Markus Eichinger, Helmut Grubmüller, and Helmut Heller

The animated GIF EGO-logo was produced with EGO (of course): it displays the trajectory of a short molecular dynamics simulation of charged carbon atoms, which are arranged to form the letters EGO, inside a box of water (of which the front half is removed so that we can see the EGO letters.

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

EGO is a program to perform molecular dynamics simulations on parallel as well as on sequential computers. Supported parallel machines include the Hitachi SR8000, CRAY-T3E, IBM-SP2, Fujitsu VPP700, Parsytec-CC under PARIX and inhomogeneous clusters of UNIX workstations under PVM or MPI. EGO also runs sequentially on any decent UNIX workstation; even Windows95/NT PC's (with a GNU-C compiler) can be used.

The energy function employed partially derives from the one used in the program X-PLOR of A. Brünger. EGO can read X-PLOR pdb, psf, and parameter files and EGO output files can be converted to X-PLOR DCD/crd files and read back into X-PLOR for further analysis of the resulting trajectories.

EGO was developed for the simulation of large molecular systems on parallel computers (under PVM, MPI or PARIX). EGO uses a multiple time step algorithm combined with a structure adapted fast multipole method for the description of long range electrostatics. The method has been demonstrated to scale linearly with the number of atoms in the range of about 40,000 atoms.

History

The animated GIF EGO-logo was produced with EGO (of course): it displays the trajectory of a short molecular dynamics simulation of charged carbon atoms, which are arranged to form the letters EGO, inside a box of water (of which the front half is removed so that we can see the EGO letters.

The first version of EGO has been developed 1988/89 by H. Grubmüller and H. Heller in the Theoretical Biophysics group of Klaus Schulten at the Technical University of Munich (TUM), Germany. It had been written in occam II and ran on a home built network of T800 transputers, called the AlterEgo computer (see picture to the right).

In the following four years H. Heller continued to work on the program (and also the AlterEgo computer hardware) in the group of Klaus Schulten at the University of Illinois at Urbana-Champaign (UIUC), Il, U.S.A. The program was translated from occam II to C and implemented on various platforms (e.g., a CM5 Connection Machine and networks of workstations). Many people helped, among them Michael Schaefer, Amitabh Sinha, Tom Bishop, Brad Banko, and Klaus Boehncke.

Beginning with 1993, EGO has been completely rewritten by Markus Eichinger supported by Helmut Grubmüller, Helmut Heller, Christoph Niedermeier, Chris Brandt, and Robert Kossman in the Theoretical Biophysics group of Paul Tavan at the Institute for Medical Optics at the Ludwig Maximilians University, Munich, Germany. The resulting program is called EGO_VIII and has been released into the public domain under the GNU general public license. Funding has been provided by the Deutsche Forschungsgemeinschaft (DFG), SFB-143 and SFB-533.

References

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:

    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, John von Neumann.

    Institute for Computing (NIC) Research Centre Jülich, Germany, 8-10 February 1999 397-402, World Scientific, Singapore 912805 (2000)

    Markus Eichinger, Helmut Grubmüller, Helmut Heller, and Paul Tavan.

    FAMUSAMM: An algorithm for rapid evaluation of electrostatic interaction in molecular dynamics simulations.

    J. Comp. Chem. 18: 1729-1749 (1997)

    [pdf]

    [postscript]

    [html]

    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.

    Publications related to EGO

      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 154-174, Singapore 912805, World Scientific (2000)

      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)

      [pdf]

      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 78-97, Springer (1998)

      [pdf]

      Markus Eichinger, Helmut Grubmüller, Helmut Heller, and Paul Tavan.

      FAMUSAMM: An algorithm for rapid evaluation of electrostatic interaction in molecular dynamics simulations.

      J. Comp. Chem. 18: 1729-1749 (1997)

      [pdf]

      [postscript]

      [html]

      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)

      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 129-138 (1995)

      Markus Eichinger.

      Paralleler schneller Multipolalgorithmus mit Mehrschrittverfahren für Molekulardynamiksimulationen.

      Diplomarbeit, Technische Universität München (April 1995)

      Helmut Grubmüller.

      Predicting slow structural transitions in macromolecular systems: conformational flooding.

      Phys. Rev. E 52: 2893-2906 (1995)

      [pdf]

      [postscript]

      [html]

      Christoph Niedermeier and Paul Tavan.

      A structure adapted multipole method for electrostatic interactions in protein dynamics.

      J. Chem. Phys. 101: 734-748 (1994)

      Amitabh B. Sinha, Klaus Schulten, and Helmut Heller.

      Performance Analysis of a Parallel Molecular Dynamics Program.

      Computer Phys. Comm. 78: 265-278 (1994)

      Helmut Grubmüller.

      Molekulardynamik von Proteinen auf langen Zeitskalen.

      PhD thesis, Technische Universität München, (Jan 1994)

      [pdf]

      [postscript]

      Helmut Heller.

      Simulation einer Lipidmembran auf einem Parallelrechner.

      PhD thesis, Technical University of Munich, Germany (December 1993)

      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)

      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)

      [pdf]

      Helmut Heller, Helmut Grubmüller, and Klaus Schulten.

      Molecular dynamics simulation on a parallel computer.

      Molecular Simulation 5: 133-165 (1990)

      [pdf]

      Helmut Grubmüller.

      Dynamiksimulation sehr großer Makromoleküle auf einem Parallelrechner.

      Diplomarbeit, Technische Universität München (1989)

      Helmut Heller.

      Dynamiksimulation sehr großer Makromoleküle am Beispiel des photosynthetischen Reaktionszentrums von Rhodopseudomonas viridis.

      Diplomarbeit, Technische Universität München (1988)

      Helmut Grubmüller, Helmut Heller, and Klaus Schulten.

      H. Grubmüller, H. Heller, and K. Schulten.

      Eine CRAY für 'jedermann'.

      mc (11): 48-65 (November 1988)

      [pdf]

      [cover]

      Apr 25, 2000

      Zur Redakteursansicht