GROMOS
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GROMOS is a force field for molecular dynamics simulation developed at the University of Groningen and 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.
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
Aliphatic CHn groups were represented as united atoms with van der Waals interactions were reparametrized on the basis of a series of molecular dynamics simulations of model liquid alkanes using long (1.6-nm) nonbonded cutoff radii. [2] This version is continually being refined and a number of different parameter sets are available.
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.
External links
- GROMOS website
- 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.
- 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.