pultar / gromosXX

md++ code

About the GROMOS software for biomolecular simulation

What is GROMOS

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. [1]. 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 GROMOS software (since 1978) members of the research groups of Wilfred van Gunsteren (Groningen, Zürich), Philippe Hünenberger (Zürich), Chris Oostenbrink (Vienna), Niels Hansen (Stuttgart) and Sereina Riniker (Zürich) have contributed.

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	Comprehensive GROMOS96 parameter set [2-5]
53A5/6	Reparameterization of polar groups [6]
54A7	Optimization of lipids [7] and protein backbone [8]
54A8	Reparameterization of charged groups [9]

GROMOS documentation

Extensive GROMOS software manuals accompanied the major releases of 1987 [10] and 1996 [11]. The functionalities of GROMOS87, GROMOS96 and GROMOS05 are summarized in the scientific literature [1, 12, 13].

The current GROMOS manual and user guide consists of nine volumes, which are available at the GROMOS website:

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 architecture and different functionalities of the current version of GROMOS are described in the a number of papers [14]-[20].

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. A basic tutorial is available in volume 7 of the GROMOS manual (see above). The files required for this tutorial, are available from the downloads page on this website. A more advanced set of tutorials can be found in [21]

Distribution of GROMOS software and manuals

Information on GROMOS is available at www.gromos.net which is owned and maintained by Biomos b.v., Laboratory of Physical Chemistry, HCI, ETH Hönggerberg, 8093 Zürich, Switzerland.

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.

References

1. 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, doi: 10.1002/jcc.20303
2. L.D. Schuler, X. Daura, W.F. van Gunsteren, An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase., J. Comput. Chem. 22 (2001) 1205-1218, doi: 10.1002/jcc.1078
3. I. Chandrasekhar, M. Kastenholz, R.D. Lins, C. Oostenbrink, L.D. Schuler, D.P. Tieleman, W.F. van Gunsteren, A consistent potential energy parameter set for lipids: Dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field, Eur. Biophys. J. 32 (2003) 67-77, doi: 10.1007/S00249-002-0269-4
4. T.A. Soares, P.H. Hnenberger, M.A. Kastenholz, V. Krutler, T. Lenz, R.D. Lins, C. Oostenbrink, W.F. van Gunsteren, An improved nucleic-acid parameter set for the GROMOS force field, J. Comput. Chem. 26 (2005) 725-737, doi: 10.1002/Jcc.20193
5. R.D. Lins, P.H. Hünenberger, A new GROMOS parameter set for hexopyranose-based cardohydrates, J. Comput. Chem. 26 (2005) 1400 - 1412, doi: 10.1002/jcc.20275
6. C. Oostenbrink, A. Villa, A.E. Mark, W.F. van Gunsteren, A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6, J. Comp. Chem. 25 (2004) 1656-1676, doi: 10.1002/jcc.20090
7. D. Poger, W.F. van Gunsteren, A.E. Mark, A new force field for simulating phosphatidylcholine bilayers, J. Comput. Chem. 31 (2010) 1117-1125, doi: 10.1002/jcc.21396
8. N. Schmid, A.P. Eichenberger, A. Choutko, S. Riniker, M. Winger, A.E. Mark, W.F. van Gunsteren, Definition and testing of the GROMOS force-field versions: 54A7 and 54B7, Eur. Biophys. J. 40 (2011) 843-856, doi: 10.1007/s00249-011-0700-9
9. M. M. Reif, P. H. Hünenberger, and C. Oostenbrink, New interaction parameters for charged amino acid side chains in the GROMOS force field, J. Chem. Theory Comput. 8 (2012) 3705-3723, doi: 10.1021/ct300156h
10. W. F. van Gunsteren and H. J. C. Berendsen, Groningen Molecular Simulation (GROMOS) Library Manual, Biomos, Groningen, The Netherlands, 1987, pp. 1-221.
11. W. F. van Gunsteren, S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. P. Scott, and I. Tironi, Biomolecular Simulation: The GROMOS96 Manual and User Guide, Vdf Hochschulverlag an der ETH Zürich, Zürich, Switzerland, 1996, p. II-30.
12. 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.
13. 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, doi: 10.1021/jp984217f
14. 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, doi: 10.1016/j.cpc.2011.12.014
15. 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, doi: 10.1002/jcc.21954
16. 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, doi: 10.1021/jp204303a
17. 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, doi: 10.1007/s10858-011-9534-0
18. 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) 3379-3390i, doi: 10.1021/ct2003622
19. S.J. Bachmann, W.F. van Gunsteren, On the compatibility of polarisable and non-polarisable models for liquid water, Mol. Phys. 112 (2014) 2761-2780, doi: 10.1080/00268976.2014.910317
20. N. Hansen, F. Heller, N Schmid, W.F. van Gunsteren, Time-averaged order parameter restraints in molecular dynamics simulations, J. Biomol. NMR 60 (2014) 169-187, doi: 10.1007/s10858-014-9866-7
21. B. Lier, C. Öhlknecht, A. de Ruiter, J. Gebhardt, W. F. van Gunsteren, C. Oostenbrink, N. Hansen, A suite of advanced tutorials for the GROMOS biomolecular simulation software [article v1.0], Living J. Comp. Mol. Sci. 2 (2020) 18552, doi: 10.33011/livecoms.2.1.18552