> When I have analyzed the corrupted rst file, the coordinates of one water
> molecule has **** in it.
>
> Do you think that substrate de-charging process might have effected a
> single water molecule?
I doubt it. Maybe the de-vdw unmasks something that the water
interacts with tho. E.g. if somehow not all atoms in the substrate
had been de-charged.
> In my case iwrap=1, was not wrapping all the water molecules around the
> substrate molecule. I am using iwrap=1 option for the first time, could you
> explain why it was not wrapping?
Wrapping is across box boundaries. If there is a strong energetic
interaction, it might send a water residue many box lengths away in
a single step, and somehow it becomes unwrappable, maybe because
of numerical problems.
Bill
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Received on Thu May 13 2010 - 10:30:05 PDT
