no, that's not what I'm saying. If you solvate like so:
"solvateBox yourUnit TIP3PBOX 0.0 1.0"
It will make a box where the closest distance between a water and your
protein or ethanol is 1.0 angstroms, and where there is a 0.0 angstrom
distance from these to the edge of the periodic box. If your ethanols
already loosely define the box, then that will be good, no?
On Mon, Dec 17, 2012 at 1:07 AM, Chinthaka Ratnaweera <cnr88.msstate.edu>wrote:
> 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
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> > >
> >
> >
> >
> > --
> > Aron Broom M.Sc
> > PhD Student
> > Department of Chemistry
> > University of Waterloo
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Chinthaka Nadun Ratnaweera
> Hand Lab Rm 1126
> Mississippi State University
> 310 Presidents Circle
> Starkville, MS 39762
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Sun Dec 16 2012 - 22:30:04 PST
