Hello Jason,
Thank you a lot for the answer!
I will keep running the molecular dynamics simulation in explicit solvent then.
Bests,
Ruth
> On 18 Sep 2015, at 13:29, Jason Swails <jason.swails.gmail.com> wrote:
>
> 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 - 06:00:05 PDT
