AMBER Archive (2004)

Subject: Re: AMBER: thermodynamic integration of ring opening

From: Bill Ross (
Date: Mon May 17 2004 - 19:10:36 CDT

> 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.

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