About the GROMOS software for biomolecular simulation
- What is GROMOS
- GROMOS documentation
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 is driven by the research group of Wilfred van Gunsteren.
Since the last official release of the GROMOS software and manual in 1996, called GROMOS96, no comprehensive release occurred. 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 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:
|45A3/4||J. 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|
|53A5/6||J. Comput. Chem. 25 (2004) 1656-1676|
|54A7||J. Comput. Chem. 31 (2010) 1117-1125|
|Eur. Biophys. J. 40 (2011) 843-856|
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 five 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.
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.
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.
Freely visible and downloadable are the Tables of Content of all 9 volumes, the contents of Volume 1, 7, 8 and 9, and the example files belonging to Volume 7. Access to the C++ source code and the contents of Volumes 2 - 6 is granted after a licence has been obtained.
A GROMOS licence will cover one year of unlimited updates and will cost between 0 and 200 € (Euro) depending on which parts of the software and documentation are to be obtained:
|Access to copy the GROMOS C++ source code including the doxygen documentation||30 €|
|Access to copy the GROMOS manuals:|
|Volume 1, Overview||0 €|
|Volume 2, Algorithms and Formulae||50 €|
|Volume 3, Force Fields||50 €|
|Volume 4, Data Structures and Formats||20 €|
|Volume 5, Program Library||20 €|
|Volume 6, Technical Details||30 €|
|Volume 7, Tutorial||0 €|
|Volume 8, Installation Guide||0 €|
|Volume 9, Index||0 €|
|Maximum cost for a one-year period:||200 €|
Licence holders may make as many copies of the code or documentation as required, but only for use in their own research group. The code and manuals are not to be released for distribution outside the licence holder's group. If the licence holder is a computer center, its customers may use the GROMOS executable code and view the licensed documentation on-line on its machines. During the licence period of one year, the licence holder will also have access to new versions and update information regarding the software and the manuals. After the one-year licence has expired, a new one-year licence is to be obtained if continued access to the source code and licenced documentation is desired.
Persons who have already paid for a GROMOS96 licence in the past year, i.e. 2010 and early 2011, will get a new GROMOS licence for free. Research groups of the ETH can get a GROMOS licence for free.
Ex-IGC members who contributed to GROMOS in the past can register themselves in the list of life-long licence holders.
All payments are executed via the internet, and software and manuals for which a licence has been obtained, is to be retrieved from the GROMOS website by the licence holder.
Licence holders and 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.