[gmx-users] how to setup the pH value

David van der Spoel spoel at xray.bmc.uu.se
Sat May 16 19:36:14 CEST 2009

Justin A. Lemkul wrote:
> Chih-Ying Lin wrote:
>> Hi
>> How to set up the pH value ?
>> what ions should I put in the solution?
> The "pH" of your simulation is governed by the protonation state you 
> assign to each of the titratable residues in your protein or other 
> molecules of interest.  There is no explicit representation of hydronium 
> ions in the force fields available in Gromacs.  Furthermore, the 
> presence of hydronium would require acid-base chemistry (proton 
> transfer) which is not possible under classical mechanics force fields.
But will be soon.
Maybe even in 4.1.

> -Justin
>> Thank you
>> Lin
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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