On Tue, Jan 19, 2010, babak minoofar wrote:
> I would like to run MD in slab geometry for solution which
> contains organic ionos and water as it is shown in the figure.
> I would like to have posetive and negative charges on the
> surface. This schematic figure shows the system looks like an
> electrochmical cell.
>
> ----------------------------
> -| ions water |+
> -| water ions |+
> -| ions water |+
> -| ions water |+
> ----------------------------
This will not be simple. Amber has only 3D periodicity, so you need to
formulate a unit cell that (when replicated in all dimensions) would give
you the required results.
[The isotropic periodic sum (IPS) technique might be manipulated for such
a simulation. But this is an advanced topic, and would require changes to the
codes, and a detailed understanding of how IPS works.]
...dac
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Received on Tue Jan 19 2010 - 06:00:02 PST
