Talk:GROMOS

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GROMOS (file format) needed

A new page GROMOS (file format) is needed, which should cross link to Chemical file format and use also the proper [[Category:Chemical file format]] category. JKW 16:05, 8 April 2006 (UTC)[reply]

Parameter sets

Not sure if appropriate, but there are a number of parameter sets for this forcefield, may be this should be mentioned? --Dr DBW (talk) 05:43, 8 September 2009 (UTC) Added new versions --Dr DBW (talk) 00:09, 1 March 2012 (UTC)[reply]

54A7 (taken 53A6 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 eneergy of hydration and new improper dihedrals) -

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.

54B7 (53B6 in vacuo changed in same manner as 53A6 to give 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.
53A5 (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) - 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.
53A6 (taken 53A5 and adjusted the partial charges to reproduce the hydration free enthalpies in water, recommended for simulations of biomolecules in explicit water) - 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.
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 - 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.
45A3 (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) - 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.
45A4 (45A3 reparameterised to improve DNA representation) - 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, [1].