[gmx-users] how to know the pH of a solution

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 29 04:39:51 CET 2011

cuong nguyen wrote:
> Dear,
> I have made a 10x10x10 box with 200 hexanoic acid molecules and fill 
> full of water.
> Please let me know how can I do to know and change the pH of this solution?

The concept of pH is ill-defined for molecular simulations, in the absence of 
the ability to transfer protons.  For classical MD, you have fixed protonation 
state and thus you can't really have "pH" in the classical sense.  I suppose you 
could get an idea of what the pH should be by measuring the ratio of 
deprotonated and protonated species in your system (i.e. Henderson-Hasselbalch).



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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