> Is there any information on how amber handles a symmetry
> condition in minimization? How would it effectively
> break the symmetry of an initial condition?
Symmetry is not considered as such. In practice, roundoff
differences might skew the calc of forces enough to break
symmetry. However it may not suffice and a local minimum
may be preserved. Even without symmetry, local minima make
minimization far less useful in finding lower-energy
conformations than low-temperature dynamics.
Bill
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Received on Mon Apr 11 2005 - 23:53:00 PDT
