[gmx-users] how to add hydrogen ions
olga.ivchenko at gmail.com
Thu Feb 3 12:47:47 CET 2011
Thank you for your reply. I am not planning to simulate proton transfer in
gromacs. Just it could be nice to see possible interaction.
2011/2/3 Erik Marklund <erikm at xray.bmc.uu.se>
> 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).
> 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.
> 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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