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
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Nov 21 2010 - 15:30:04 PST
