[gmx-users] how to add hydrogen ions

[Erik Marklund]

Mark Abraham skrev 2011-02-03 11.59:
> On 3/02/2011 9:18 PM, Olga Ivchenko wrote:
>> Dear Gromacs Users,
>>
>> I would like to replace some of my water molecules with H+ ions, or 
>> add hydrogen ions to my water box. Please could you advice me how to 
>> do it?
>
> I'm not aware of any force field that implements hydrogen cation 
> (because it is unphysical) or hydronium cation (because it would 
> immediately take you to an impossible pH, and also not be a sound 
> model of hydrogen transfer in real water).
>
> Mark
There are several articles out there where an excess hydronium in water 
has been simulated. See e.g. the work of Lill and Holms, or Schmitt and 
Voth.

Regards,

-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
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erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/