Re: AMBER: thermodynamic integration of ring opening

From: M. L. Dodson <>
Date: Tue, 18 May 2004 07:33:28 -0500

On Monday 17 May 2004 07:10 pm, Bill Ross wrote:
> > This is an inherently
> > quantum mechanical "event" you are trying to simulate with a
> > classical mechanical method. What do others think?
> The method seems to be generally accepted, if not the results
> :-) Another method is to disappear the whole residue while
> phasing in the replacement; Kollman group considered it years
> ago and stuck with the current method.
> I'm not a chemist, but the QM nature of the change seems like a
> red herring, in that the bond breaking itself is not being
> simulated; rather statistics are being generated on the
> transition between two realistic states - the nature of the
> transition should not affect the energy difference between the
> states. The energy barrier itself is not addressed by this
> method unless one were to find a desired intermediate state and
> perturb to it.
> Bill

OK, seems reasonable to me. The method would be another example
of the thermodynamic idea of "it doesn't matter what the path
between them is, only the properties of the two end states" then,

Bud Dodson
M. L. Dodson                      
409-772-2178                                FAX: 409-772-1790
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Received on Tue May 18 2004 - 13:53:00 PDT
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