The minimal distance from the solute to the boundary was set to 15 A.
The dimensions of the water box are 157x150x128 A^3.
Wei
On Fri, Jul 22, 2011 at 1:51 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>> After I solvated my protein, I used "addIons" to add ions to the
>> system to reach certain ion concentration. I found that some ions were
>> placed outside of the water box. Is this normal? When I used AMBER8
>> long time ago, this did not happen. I was wondering if this is
>> something with the new version of AmberTools.
>
> I wonder how big the water box is. Addions uses a grid based on
> a given distance from the solute, and a small box might fall
> within that distance.
>
> Bill
>
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Received on Fri Jul 22 2011 - 14:00:06 PDT
