AMBER Archive (2008)

Subject: Re: AMBER: D2O

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Thu Sep 11 2008 - 09:32:03 CDT

I will simulate a system which the solutes embeded in the D2O solution.

Am I suggested using Amber package to do so?
or, no....

Thank you
Lin

----- Original Message -----
From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
Date: Tuesday, September 9, 2008 4:19 pm
Subject: Re: AMBER: D2O
To: amber_at_scripps.edu

> but for what reason? what are you trying to learn?
>
> On Tue, Sep 9, 2008 at 3:59 PM, Chih-Ying Lin <chihying_at_usc.edu>
> wrote:>
> >
> > solute embeded in the D2O solution, instead of H2O solution
> > what is the suggestion for this?
> >
> > ----- Original Message -----
> > From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> > Date: Tuesday, September 9, 2008 11:21 am
> > Subject: Re: AMBER: D2O
> > To: amber_at_scripps.edu
> >
> >> it's important to first clarify to yourself and us what
> properties of
> >> D2O you are trying to reproduce, as compared to H2O. for
> example, are
> >> you looking at H/D exchange rates in NMR, or perhaps enzymatic
> KIE, or
> >> something else? each of these would require a different approach
> (if>> they are even tractable at all)
> >>
> >> On Tue, Sep 9, 2008 at 1:00 PM, Chih-Ying Lin <chihying_at_usc.edu>
> >> wrote:>
> >> >
> >> > Hi
> >> > Does amber support D2O simulation?
> >> > What is the difference between H2O simulation and D2O simulation?
> >> >
> >> > And, how about the force field paramters of D2O?
> >> >
> >> > How to simulate the D2O system instead of H2O?
> >> >
> >> > Thank you
> >> > Lin
> >> > ---------------------------------------------------------------
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>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
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> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
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