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.
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[edit] Versions
[edit] 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]
[edit] 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 (1.6-nm) nonbonded cutoff radii.[4] This version is continually being refined and a number of different parameter sets are available.
[edit] GROMOS05
An updated version of the simulation package was introduced in 2005.[5]
[edit] GROMOS11
The current GROMOS release is dated in May 2011.
[edit] See also
- GROMACS
- MOSCITO
- Ascalaph Designer
- Software for molecular mechanics modeling
- Force field implementation
[edit] 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
