AMBER Archive (2008)

Subject: Re: AMBER: D2O

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Sep 09 2008 - 13:21:37 CDT

On Tue, Sep 09, 2008, Chih-Ying Lin wrote:
>
> Does amber support D2O simulation?
> What is the difference between H2O simulation and D2O simulation?

I think this is too broad a question to answer on the email list. You
will need to study some basic statistical mechanics on your own.

Briefly: you could run a *classical* simulation in D2O by simply changing the
masses of the hydrogen atoms. This would not be a good model, however, for
the real (i.e experimental) differences between H2O and D2O.

You could run PIMD and related calculations to get quantum nuclear
dynamics. In principle, this could give very accurate results.
However, the q-SPCfw model in Amber has not yet been tested much for D2O
-- maybe Francesco will have some comments here.

So, although it is in principle possible, a serious effort would be required
here. It is not a generally-supported option in Amber.

...dac

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