Minimization is only to a local minimum, so only a minimum amount
of it is worthwhile. Usually 500 steps is plenty. It's like you are
sitting in a chair, and you let yourself relax there. It would be
much lower energy to lie down, but this would involve getting up first.
Low-temperature dynamics will get you to lower energies 99.999% of
the time with biomolecular-scale systems. If the system is distorted
by e.g. hand-building artifacts, then it can be worth doing successive
minimizations with parts held fixed (leap is good for this), but
normally I don't think there is much value in minimizing solute then
solvent.
Bill
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Received on Tue Aug 09 2005 - 19:53:01 PDT
