but if the ethanols are already making up roughly the box size you want,
can't you just give no boundary, or close to it?
On Mon, Dec 17, 2012 at 12:14 AM, Chinthaka Ratnaweera <cnr88.msstate.edu>wrote:
> I have to use certain concentration of ethanol/water mixture for my protein
> model. I couldn't find ethanol solvatebox in amber. so I randomly added
> desired number of ethanol molecules to a given box size (using packmol).
> But now the problem is when I add water solvatebox (tip3p), ethanols also
> consider as a part of the solute and count the distance for boundaries from
> ethanol molecules making the box size much larger which I do not want.
> Appreciate if any one can guide me to solve this problem. Thank you.
>
> Chinthaka
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Sun Dec 16 2012 - 22:30:03 PST
