[gmx-users] addition of hydronium ion in simulation box

[André Farias de Moura]

for instance, take a look at this reference by Michele Parrinello to see
some general remarks on how you should proceed if you really want to
describe the dynamics of protons within a water channel:

http://www.nature.com/nature/journal/v392/n6673/full/392258a0.html

we have already done some simplified simulation for teaching purposes,
placing a single H3O+ within a water nanodroplet with a few tens of
(neutral) water molecules, and then performing a short molecular dynamics
simulation with the semiempirical method MSINDO. the original H3O+ looses
one of its identical H atoms, which becomes attached to a neighboring H2O
molecule, which now has 3 identical H atoms, and then looses one of them to
another neighboring H2O molecule and so on.

I'm still testing it, but DFTB should do the trick as well.

On Mon, Sep 21, 2015 at 11:36 PM, André Farias de Moura <moura at ufscar.br>
wrote:

> It's not H3O+ that diffuses away, it is the H+ that moves from one
> molecule to the next instead.
>
> and protons behave quantum mechanically, so you should not expect any
> classical model to be able to properly describe their dynamics.
>
> for instance, you must consider that a proton may just tunnel from one
> water molecule to the next with an appreciable probability due to the
> combination of small mass, energy barrier height and short distance between
> neighboring water molecules (just like the particle in a square well in the
> standard textbooks of quantum chemistry).
>
> On Mon, Sep 21, 2015 at 10:49 PM, Padmani Sandhu <
> padmanisandhu09 at gmail.com> wrote:
>
>> Hello justin,
>>
>> Thanks, actually I want to study movement of protons along the lenght of a
>> water channel.
>>
>>
>> Regards,
>>
>>
>> Padmani
>>
>>
>>
>> On Monday, September 21, 2015, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
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>
>
> --
> _____________
>
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
>



-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090