[gmx-users] how to setup the pH value

Justin A. Lemkul jalemkul at vt.edu
Sat May 16 19:32:41 CEST 2009

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.


> Thank you
> Lin
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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