On Mon, Apr 04, 2011, gromacs wrote:
>
> Does Amber 11 contain OPLS-AA force-field?
No.
> Can i simulate polarisable ions （with polarisable water）？
Amber's only built-in polarizable force fields are ff02pol.r1 and amoeba.
Both allow polarizable ions in water, but my understanding(?) is that the
parmaeters in ff02pol.r1 are not well-tested. Someone who knows more might
want to chime in here.
>
> Which force-field is suitable for run just water with ions?
Depends on your definition of "suitable", and a full discussion is beyond the
scope of an email list. You might want to review the performance of our
simpler, non-polarizable models:
%A I.S. Joung
%A T.E. Cheatham, III
%T Determination of alkali and halide monovalent ion parameters for use in
explicitly solvated biomolecular simulations
%J J. Phys. Chem. B
%V 112
%P 9020-9041
%D 2008
%A I.S. Joung
%A T.E. Cheatham, III
%T Molecular dynamics simulations of the dynamic and energetic properties of
alkali and halide ions using water-model-specific ion parameters
%J J. Phys. Chem. B
%V 113
%P 13279-13290
%D 2009
This may help you decide whether or not to look at more complex force fields.
Some information on the latter is here:
%A A. Grossfield
%A P. Ren
%A J.W. Ponder
%T Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field
%J J. Am. Chem. Soc.
%V 125
%P 15671-15682
%D 2003
Note that all of this relates to monovalent ions. The situation for divalent
ions is more complex.
...dac
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Received on Mon Apr 04 2011 - 05:30:02 PDT
