On Fri, Sep 18, 2015 at 4:52 AM, Ruth Helena Tichauer <rhtichau.laas.fr>
wrote:
> Hello Jason,
>
> Thank you for the explanations.
>
> It’s absolutely right that water exchanges readily but as I was running
> the calculation in implicit solvent, I thought that the water molecule in
> the active site couldn’t be replaced by another, ergo I wouldn’t be able to
> get the information I’m looking for.
>
This makes it even harder to keep the water near the reacting center!
With implicit solvent, the water will simply diffuse away, replaced by the
implicit representation of a water molecule.
Using implicit solvent here will be quite difficult to do "correctly".
>
> Does the “variable solvent “ QM/MM approach works in implicit solvent?
>
No. As one water molecule moves out of the QM region and another moves
in, the water that is treated with QM switches (at least, that's my very
general understanding). Obviously if no water replaces the one diffusing
away, this cannot happen.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 18 2015 - 04:30:04 PDT
