[gmx-users] Adding proton using genion to study proton transfer reaction

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Oct 10 08:47:29 CEST 2013

Hi DeepaK,

You should be aware that excess protons are not floating around freely
among a bunch of H2O. Whatever reasoning along this line is physically
meaningless (including thinking of a mixture of H3O+, H2O, OH-). This is
the realm of QM.



On Thu, Oct 10, 2013 at 8:05 AM, Deepak Ojha <alwaysinthemind at gmail.com>wrote:

> Dear GMxers,
> I want to simulate the proton transfer reaction in bulk water using
> gromacs.I am not aware how to add proton using genion.Is it possible to add
> excess protons like other ions.I could not find proton in ions.itp.
> If anybody can guide me about the same.
> Thanks
> DeepaK Ojha
> School Of Chemistry
> "Selfishness is not living as one wishes to live, it is asking others to
> live as one wishes to live"
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Tsjerk A. Wassenaar, Ph.D.

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