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

[André Farias de Moura]

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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> --
> *Padmani sandhu*
> *Research Scholar,*
> *Center for Computational Biology and Bioinformatics,*
> *Central University of Himachal Pradesh,*
> *Temporary Academic Block, Shahpur *
> *Pin 176206, District Kangra,*
> *Himachal Pradesh, India*
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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