Hello,
I want to start an MD simulation of a silica particle of size 5-10 nm
in
aequous solution, possibly also with a few Na+ ions floating around. I
have a sample PDB file containing the structure of a silica
nanoparticle,
and have tried to make a box containing the nanoparticle and some water
molecules using the 'genbox' utility program of GROMACS.
The problem arises when defining the parameters which determine how
the
atoms will interact. Does anyone have a good set of general parameters
for
such a system ? I am aware of the the work of Wensink and Hoffmann
[Langmuir 16, 7392 (2000)], but their scheme relies on a partitioning
of
the system into crystal, surface and water atoms and I do not know how
such a partitioning could be done in my case so as to best use their
parameterization.
I'm not 100% tied to using GROMACS (any freely available and capable
MD
code will do for some initial investigations). I would be grateful for
any
advice on alternatives.
My investigations are intended to look into the behaviour in solution
of
silica nanoparticles formed by polymerization in solutions of sodium
silicates, including nucleation, growth, formation of charged
nanoparticles (and consequently double layers) and the effect of
solution
pH on this process and the detailed effects on nanoparticle surface
charge
density. The list above is long, I realize, but I would very much
appreciate some pointers on how to get started quickly into these
investigations.
Many thanks in advance,
Steve Kirk
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