[gmx-users] force field parameters for hydronium

David van der Spoel spoel at xray.bmc.uu.se
Mon Apr 28 21:19:15 CEST 2008

Vasilii Artyukhov wrote:
> 2008/4/28 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>:
>      Trying to model hydronium is a pretty flawed thing to do, since the
>     hydrogens in real water are labile - so the molecule you'd label as
>     "hydronium" moves much faster than any atoms do. 
> I actually seem to remember reading something about some dissociative 
> water models that could exchange protons between molecules, so that one 
> could really have something like a pH in the simulation... doesn't 
> really account for the quantum stuff like tunneling, though :)

@Article{ Mahadevan2007a,
   author =	 "T. S. Mahadevan and S. H. Garofalini",
   title =	 "Dissociative Water Potential for Molecular Dynamics
   journal =	 "J. Phys. Chem. B",
   year =	 2007,
   url =
   doi =		 "10.1021/jp072530o",
   abstract =	 "A new interatomic potential for dissociative water
                   was developed for use in molecular dynamics
                   simulations. The simulations use a multibody
                   potential, with both pair and three-body terms, and
                   the Wolf summation method for the long-range Coulomb
                   interactions. A major feature in the potential is
                   the change in the short-range O-H repulsive
                   interaction as a function of temperature and/or
                   pressure in order to reproduce the
                   density-temperature curve between 273 K and 373 at 1
                   atm, as well as high-pressure data at various
                   temperatures. Using only the change in this one
                   parameter, the simulations also reproduce
                   room-temperature properties of water, such as the
                   structure, cohesive energy, diffusion constant, and
                   vibrational spectrum, as well as the liquid-vapor
                   coexistence curve. Although the water molecules
                   could dissociate, no dissociation is observed at
                   room temperature. However, behavior of the hydronium
                   ion was studied by introduction of an extra H+ into
                   a cluster of water molecules. Both Eigen and Zundel
                   configurations, as well as more complex
                   configurations, are observed in the migration of the

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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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