See Adrian's response:
> TIP3P waters are strange objects inside amber, since the atoms have
> particular names, bonds, etc.
>
> Also, what do you expect to see in the simulation ? No thermodynamic
> property can change when the masses change, so the only possible change
> would be in time scales, which are very unreliable anyway.
>
> Adrian
You could, of course, simply change the mass of the H's to match D and see
what happens, but I would not expect to get much meaningful information from
the simulation. Of course, SHAKE should be applied to the various water
models, anyway, which eliminates the H-degrees of freedom. Thus, the only
difference between a D2O water model and a normal water model will be the
molecular mass of 20 g/mol vs. 18 g/mol.
You can also change the bond force constants, but TIP3P is defined strangely
(O-H, O-H, and H-H bonds to maintain geometry), with no VDW parameters on
the H atoms. They are designed to be treated with SHAKE, or you'll probably
get H-atoms collapsing into a strongly negative atom. Using SHAKE will
render any modifications you make to the bond force constants meaningless,
since those degrees of freedom are eliminated, anyway.
Good luck,
Jason
On Sun, Nov 21, 2010 at 6:04 PM, setyanto md <stwahyudi.md.gmail.com> wrote:
> I curious with Philipe pinard question.
>
> Actually I want to do so.
>
> What should I do to change H2O with D20 box ?
>
> In real experiment using neutron (small angle neutron scattering - SANS)
> usually people use D20 or D2O/H20 percentage instead of only H2O. This is
> related with different scattering length between D2O and H2O. I would to
> have protein environment similar with environment in SANS experiment.
>
> Thank you for your attention
>
> Setyanto Tri W
>
>
> On Wed, Nov 17, 2010 at 9:00 PM, Adrian Roitberg <roitberg.qtp.ufl.edu
> >wrote:
>
> > what did you exactly do, and how do you know it did not work ?
> >
> > TIP3P waters are strange objects inside amber, since the atoms have
> > particular names, bonds, etc.
> >
> > Also, what do you expect to see in the simulation ? No thermodynamic
> > property can change when the masses change, so the only possible change
> > would be in time scales, which are very unreliable anyway.
> >
> > Adrian
> >
> >
> > On 11/17/10 2:56 PM, Philippe Pinard wrote:
> > > Hi amber users
> > >
> > >
> > > I would like to ask about the possibility to solvate my molecule with
> D2O
> > > TIP3PBOX water, does this just require changing the H mass in a new
> > frcmod file,
> > > it did not work for me!
> > > any help much appreciated
> > > PP
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> > --
> > Dr. Adrian E. Roitberg
> > Associate Professor
> > Quantum Theory Project, Department of Chemistry
> > University of Florida
> >
> > Senior Editor. Journal of Physical Chemistry.
> >
> > on Sabbatical in Barcelona until August 2011.
> > Email roitberg.ufl.edu
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Nov 21 2010 - 15:30:05 PST
