Thanks, But I think I need the periodic boundary conditions for the
simulation. Just adding ethanols will not create periodic box.
On Sun, Dec 16, 2012 at 11:58 PM, Aron Broom <broomsday.gmail.com> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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>
--
Chinthaka Nadun Ratnaweera
Hand Lab Rm 1126
Mississippi State University
310 Presidents Circle
Starkville, MS 39762
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Received on Sun Dec 16 2012 - 22:30:03 PST
