Ok This I can test. But I dought whether this will make the correct size of
box since I am using 3 ethanol molecules for each 10000 water molecules.
On Mon, Dec 17, 2012 at 12:14 AM, Aron Broom <broomsday.gmail.com> wrote:
> 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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> > > >
> > >
> > >
> > >
> > > --
> > > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
> _______________________________________________
> AMBER mailing list
> 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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Received on Sun Dec 16 2012 - 23:00:02 PST
