GROMOS
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GROMOS is a force field for molecular dynamics simulation developed at the University of Groningen and at Computer-Aided Chemistry Group at the Laboratory for Physical Chemistry at the ETH Zurich.
The united atom force field was optimized with respect to the condensed phase properties of alkanes.
GROMOS is also the name for the molecular dynamics simulation package associated with this force field.
Contents
Versions
GROMOS87
Aliphatic and aromatic hydrogen atoms were included implicitly by representing the carbon atom and attached hydrogen atoms as a single group centered on the carbon atom, a united atom force field. The van der Waals parameters were derived from calculation of the crystal structures of hydrocarbons and calculations on amino acids using short (0.8 nm) nonbonded cutoff radii.[1]
GROMOS96
A substantial rewrite of the simulation package was released in 1996.[2][3] The force field was also improved, e.g. in the following way: aliphatic CHn 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 alkanes using long (1.4 nm) nonbonded cutoff radii.[4] This version is continually being refined and a number of different parameter sets are available. GROMOS96, apart from having a study in molecular dynamics, also includes a study of stochastic dynamics and also of energy minimization. The energy minimization component was also part of the last GROMOS, named GROMOS87. GROMOS96 was planned and conceived during a time period of 20 months. This package is design within 40 different programs, and each of them have 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 simulation package was introduced in 2005.[5]
GROMOS11
The current GROMOS release is dated in May 2011.
Parameter Sets
Some of the forcefield parameter sets that are based on the GROMOS forcefield. A-version is for application to aqueous or apolar solutions of proteins, nucleotides and sugars and B-version is for simulation of isolated molecules (gas phase).
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- 54A7[6] - 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[6] - 53B6 in vacuo taken and changed in same manner as 53A6 to 54A7.
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- 53A5[7] - 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[7] - 53A5 taken and adjusted partial charges to reproduce hydration free enthalpies in water, recommended for simulations of biomolecules in explicit water.
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- 45A3[8] - suitable for application to lipid aggregates such as membranes and micelles, for mixed systems of aliphatics with or without water, for polymers, and other apolar systems that may interact with different biomolecules.
- 45A4[9] - 45A3 reparameterised to improve DNA representation.
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See also
- GROMACS
- MOSCITO
- Ascalaph Designer
- Software for molecular mechanics modeling
- Force field implementation
References
- ↑ W. F. van Gunsteren and H. J. C. Berendsen, Groningen Molecular Simulation (GROMOS) Library Manual, BIOMOS b.v., Groningen, 1987.
- ↑ 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.
- ↑ "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.
- ↑ "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 PMID 16211540
- ↑ 6.0 6.1 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 [1].
- ↑ 7.0 7.1 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 [2].
- ↑ 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 [3].
- ↑ 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, [4].
- ↑ 10.0 10.1 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.
