AMBER Archive (2004)

Subject: Re: AMBER: Parameters for deuterium

From: David A. Case (case_at_scripps.edu)
Date: Tue Jan 06 2004 - 10:32:14 CST

On Tue, Jan 06, 2004, Charlie Laughton wrote:
>
> I'd appreciate any thoughts/experiences on simulations incorporating
> deuterium (C-D or O-D bonds). Is it enough just to take corresponding H
> parameters and up the mass?
>

The force field is unchanged, and the masses do change. But you need to
remember that in classical mechanics, the distribution of configurations
is independent of the atomic masses, and so there are no "isotope effects" in
the usual sense. This means that the properties of MD simulations are not
affected by changing H to D. You would need to incorporate quantum effects
(especially zero-point motion) to see the real differences upon isotope
substitution.

The one place where a simple classical model would work is for vibrational
frequencies: here if you change the atomic masses, you would see the
appropriate change in frequencies.

..hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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10550 N. Torrey Pines Rd.         |  home page:                   
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