No water at the beginning. This (ions outside the box) did not happen
using AMBER8.
Wei
On Sat, Jul 23, 2011 at 1:45 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> The grid that I programmed extended much less than that from the solute,
> maybe 6A. If that is still the case, the presence of ions outside the box
> implies that one or more waters might be seen as solute. Were there any
> waters in your loaded pdb file?
>
> Bill
>
> ---
>
> 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 Sat Jul 23 2011 - 14:30:02 PDT
