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About the GROMOS software for biomolecular simulation

  1. What is GROMOS
  2. GROMOS™ is an acronym of the GROningen MOlecular Simulation computer program package, which has been developed since 1978 for the dynamic modelling of (bio)molecules, until 1990 at the University of Groningen, The Netherlands, and since then at the ETH, the Swiss Federal Institute of Technology, in Zürich, Switzerland. Its development was driven by the research group of Wilfred van Gunsteren. Currently, the development is shared between him and the research groups of Philippe Hünenberger and Sereina Riniker at the ETH, of Chris Oostenbrink at the University of Natural Resources and Life Sciences in Vienna, Austria, and of Niels Hansen at the University of Stuttgart, Stuttgart, Germany.

    Since the last official release of the GROMOS software and manual in 1996, called GROMOS96, no comprehensive release occurred till 2011. Yet the GROMOS software has seen a steady development since 1996, see e.g. Christen et al. J. Comput. Chem. 26 (2005) 1719. The programming language has been changed from FORTRAN to C++, the documentation has been put into electronic form, and many new features have been included in the software.

    To the development of the new code and manuals released in 2011 many current and former members of the research group for Informatikgestützte Chemie (igc) have contributed : Jane Allison, Dirk Bakowies, Ulf Börjesson, Roland Bürgi, Alexandra Choutko, Clara Christ, Markus Christen, Jozica Dolenc, Andreas Eichenberger, Daan Geerke, Alice Glättli, Halvor Hansen, Bruno Horta, Philippe Hünenberger, Mika Kastenholz, Anna-Pitschna Kunz, Katharina Meier, Chris Oostenbrink, Christine Peter, Maria Reif, Sereina Riniker, Heiko Schäfer, Nathan Schmid, Denise Steiner, Dongqi Wang, Haibo Yu, to mention a few.

    The GROMOS software is to be distinguished from the GROMOS force fields for biomolecular systems, of which the latest versions are coded as:

    45A3/4J. Comput. Chem. 22 (2001) 1205-1218
    Eur. Biophys. J. 32 (2003) 67-77
    J. Comput. Chem. 26 (2005) 725-737
    J. Comput. Chem. 26 (2005) 1400-1412
    53A5/6J. Comput. Chem. 25 (2004) 1656-1676
    54A7J. Comput. Chem. 31 (2010) 1117-1125
    Eur. Biophys. J. 40 (2011) 843-856
    54A8J. Chem. Theory Comput. 8 (2012) 3705-3723

  3. GROMOS documentation
  4. The GROMOS software manuals that accompanied the major releases of 1987 and 1996 are:

    • W. F. van Gunsteren and H. J. C. Berendsen, Groningen Molecular Simulation (GROMOS) Library Manual, Biomos, Groningen, The Netherlands, 1987, pp. 1-221.
    • W. F. van Gunsteren, S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. P. Scott, and I. G. Tironi, Biomolecular Simulation: The GROMOS96 Manual and User Guide, Vdf Hochschulverlag AG an der ETH Zürich, Zürich, Switzerland, 1996, pp. 1-1042.

    The current GROMOS manual and user guide consists of 9 volumes:

    The GROMOS Software for (Bio)Molecular Simulation

    • Volume 1: About the GROMOS Package: Overview
    • Volume 2: Algorithms and Formulae for Modelling of Molecular Systems
    • Volume 3: Force Fields and Topology Data Set
    • Volume 4: Data Structures and Formats
    • Volume 5: Program Library Manual
    • Volume 6: Technical Details
    • Volume 7: Tutorial with Examples
    • Volume 8: Installation Guide
    • Volume 9: Index

    The functionalities of GROMOS87, GROMOS96 and GROMOS05 have been summarized in

    • W. R. P. Scott and W. F. van Gunsteren, The GROMOS Software Package for Biomolecular Simulations, In: Methods and Techniques in Computational Chemistry: METECC-95, E. Clementi and G. Corongiu editors, STEF, Cagliari, Italy, 1995, pp. 397-434.
    • W. R. P. Scott, P. H. Hünenberger, I. G. Tironi, A. E. Mark, S. R. Billeter, J. Fennen, A. E. Torda, T. Huber, P. Krüger, and W. F. van Gunsteren, The GROMOS Biomolecular Simulation Package, J. Phys. Chem. A 103 (1999) 3596-3607.
    • M. Christen, P. H. Hünenberger, D. Bakowies, R. Baron, R. Bürgi, D. P. Geerke, T. N. Heinz, M. A. Kastenholz, V. Kräutler, C. Oostenbrink, C. Peter, D. Trzesniak, and W. F. van Gunsteren, The GROMOS Software for Biomolecular Simulation: GROMOS05, J. Comput. Chem. 26 (2005) 1719-1751.

    The architecture and different functionalities of the current version of GROMOS are described in the following papers:

    • N. Schmid, C. D. Christ, M. Christen, A. P. Eichenberger, and W. F. van Gunsteren, Architecture, Implementation and Parallelisation of the GROMOS Software for Biomolecular Simulation, Comp. Phys. Commun. 183 (2012) 890-903.
    • A. P. E. Kunz, J. R. Allison, D. P. Geerke, B. A. C. Horta, P. H. Hünenberger, S. Riniker, N. Schmid, and W. F. van Gunsteren, New Functionalities in the GROMOS Biomolecular Simulation Software, J. Comput. Chem. 33 (2012) 340-353.
    • S. Riniker, C. D. Christ, H. S. Hansen, P. H. Hünenberger, C. Oostenbrink, D. Steiner, and W. F. van Gunsteren, Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation and Conformational Transitions using the GROMOS Software, J. Phys. Chem. B 115 (2011) 13570-13577.
    • N. Schmid, J. R. Allison, J. Dolenc, A. P. Eichenberger, A. P. E. Kunz, and W. F. van Gunsteren, Biomolecular Structure Refinement using the GROMOS Simulation Software, J. Biomol. NMR 51 (2011) 265-281.
    • A. P. Eichenberger, J. R. Allison, J. Dolenc, D. P. Geerke, B. A. C. Horta, K. Meier, C. Oostenbrink, N. Schmid, D. Steiner, D. Wang, and W. F. van Gunsteren, The GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories, J. Chem. Theory Comput. 7 (2011) 3379-3390.
    • S. J. Bachmann, and W. F. van Gunsteren, On the compatibility of polarisable and non-polarisable models for liquid water, Mol. Phys. 112 (2014) 2761-2780.
    • N. Hansen, F. Heller, N. Schmid, and W. F. van Gunsteren, Time-averaged order parameter restraints in molecular dynamics simulations, J. Biomol. NMR 60 (2014) 169-187.

    The GROMOS C++ code is documented in the code in the form of a doxygen documentation. It is accompanied by make files, etc. and by example files.

  5. Distribution of GROMOS software and manuals
  6. Information on GROMOS will be kept on this website which is owned and maintained by Biomos b.v., Laboratory of Physical Chemistry, HCI, ETH Hönggerberg, 8093 Zürich, Switzerland.

    A GROMOS license will be issued for free upon registration of a user at this site. This reistration allows Biomos to contact them if needed.

    GROMOS users are obliged to properly acknowledge the use of the software, e.g. by referencing one or more of the mentioned scientific papers.

    Although we are continuously testing the GROMOS software, it goes without saying that we cannot be held responsible for any damage caused by errors in the software or data files.