> when adding explicit solvent and then ions to neutralize the system, do
> the ion atoms always come after the solute atoms in the topology file
> regardless if one adds the explicit solvent first then counter ions in
> tleap?
For optimization of calcs, all solute molecules appear before all
solute ones. This is independant of the order of adding ions/water.
I believe ions follow other solute molecules due to having fewer
atoms. In any case, I think you would have to look at leap code
to change the order of things.
Bill
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Received on Tue Aug 16 2011 - 16:30:02 PDT
