> Thus, the minimization is done to try and compact the water molecules and
> get rid of air bubbles. I'm not sure if that is what I am actually
> accomplishing, but that is the general idea.
Minimization just reduces excessive initial steric clashes, bad bonds,
etc. - it does not do very much that is visible unless your starting
model is really bad. Dynamics with NPT will get rid of the bubbles.
Bill
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Received on Mon Apr 04 2011 - 21:00:02 PDT
