[gmx-users] how to add hydrogen ions

Erik Marklund erikm at xray.bmc.uu.se
Thu Feb 3 12:02:18 CET 2011

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 


Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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