GROningen MOlecular Simulation (GROMOS) is the name of a force field for molecular dynamics simulation, and a related computer software package, which has been developed until 1990 at the University of Groningen, and at the Computer-Aided Chemistry Group[ Computer-Aided Chemistry Group, ETH Zurich] at the Laboratory for Physical Chemistry[ Laboratory for Physical Chemistry, ETH Zurich] at the Swiss Federal Institute of Technology (ETH Zurich). At Groningen, Herman Berendsen was involved in its development.
The united atom force field was optimized with respect to the condensed phase properties of .
Versions
GROMOS87
Aliphatic and aromatic
hydrogen atoms were included implicitly by representing the
carbon atom and attached hydrogen atoms as one group centered on the carbon atom, a united atom force field. The van der Waals force parameters were derived from calculations of the crystal structures of
, and on
using short (0.8 nm) nonbonded cutoff radii.
[W. F. van Gunsteren and H. J. C. Berendsen, Groningen Molecular Simulation (GROMOS) Library Manual, BIOMOS b.v., Groningen, 1987.]
GROMOS96
In 1996, a substantial rewrite of the software package was released.
[van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; vdf Hochschulverlag AG an der ETH Zürich and BIOMOS b.v.: Zürich, Groningen, 1996.]["The GROMOS Biomolecular Simulation Program Package", W. R. P. Scott, P. H. Huenenberger, I. G. Tironi, A. E. Mark, S. R. Billeter, J. Fennen, A. E. Torda, T. Huber, P. Krueger and W. F. van Gunsteren. J. Phys. Chem. A, 103, 3596–3607.] The force field was also improved, e.g., in the following way: aliphatic CH
n groups were represented as united atoms with van der Waals interactions reparametrized on the basis of a series of molecular dynamics simulations of model liquid
using long (1.4 nm) nonbonded cutoff radii.
["An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase". Journal of Computational Chemistry 22 (11), August 2001, 1205–1218 by Lukas D. Schuler, Xavier Daura, Wilfred F. van Gunsteren.] This version is continually being refined and several different parameter sets are available. GROMOS96 includes studies of molecular dynamics, stochastic dynamics, and energy minimization. The energy component was also part of the prior GROMOS, named GROMOS87. GROMOS96 was planned and conceived during a time of 20 months. The package is made of 40 different programs, each with a different essential function. An example of two important programs within the GROMOS96 are PROGMT, in charge of constructing molecular topology and also PROPMT, changing the classical molecular topology into the path-integral molecular topology.
GROMOS05
An updated version of the software package was introduced in 2005.
["The GROMOS software for biomolecular simulation: GROMOS05". Christen M, Hünenberger PH, Bakowies D, Baron R, Bürgi R, Geerke DP, Heinz TN, Kastenholz MA, Kräutler V, Oostenbrink C, Peter C, Trzesniak D, van Gunsteren WF. J Comput Chem 26 (16): 1719–51 ]
GROMOS11 version 1.6.1
The current GROMOS version was released in November 2023 and updated in April 2024. New functionalities such as support fir virtual atoms with non-bonded interactions, shifted reaction-field,
buffer region neural network,
combined TI with (A-)EDS
and selective Gaussian accelerated MD.
Parameter sets
Some of the force field parameter sets that are based on the GROMOS force field. The A-version applies to aqueous or
Hydrophobe solutions of
,
, and
. The B-version applies to isolated
(gas phase).
54
-
54A8
-
54A7
[Schmid N., Eichenberger A., Choutko A., Riniker S., Winger M., Mark A. & van Gunsteren W., "Definition and testing of the GROMOS force-field versions 54A7 and 54B7", European Biophysics Journal, 40(7), (2011), 843–856 [3].] - 53A6 taken and adjusted torsional angle terms to better reproduce helical propensities, altered N–H, C=O repulsion, new CH3 charge group, parameterisation of Na+ and Cl− to improve free energy of hydration and new improper dihedrals.
-
54B7
53
-
53A5
[Oostenbrink C., Villa, A., Mark, A. E., and van Gunsteren, W., "A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6", Journal of Computational Chemistry, 25, (2004), 1656–1676 [4].] - optimised by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane, is an expansion and renumbering of 45A3.
-
53A6
45
-
45A3
[Schuler, L. D., Daura, X., and van Gusteren, W. F., An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase, Journal of Computational Chemistry 22(11), (2001), 1205–1218 [5].] - suitable to apply to lipid aggregates such as and , for mixed systems of aliphatics with or without water, for , and other apolar systems that may interact with different biomolecules.
-
45A4
[Soares, T. A., Hünenberger, P. H., Kastenholz, M. A., Kräutler, V., Lenz, T., Lins, R. D., Oostenbrink, C., and van Gunsteren, W. F., An improved nucleic acid parameter set for the GROMOS force field, Journal of Computational Chemistry, 26(7), (2005), 725–737, [6].] - 45A3 reparameterised to improve DNA representation.
43
-
43A1
[van Gunsteren, W. F., Billeter, S. R., Eking, A. A., Hiinenberger, P. H., Kriiger, P., Mark, A. E., Scott, W. R. P. and Tironi, I. G., Biomolecular Simulation, The GROMOS96 Manual and User Guide, vdf Hochschulverlag AG an der ETH Ziirich and BIOMOS b.v., Zurich, Groningen, 1996.]
-
43A2
See also
-
GROMOS
-
Ascalaph Designer
-
Comparison of software for molecular mechanics modeling
-
Comparison of force field implementations
External links
