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

Dallas Warren Dallas.Warren at monash.edu
Tue Nov 29 05:31:37 CET 2011

> Actually, I am trying to solve problem between C6H13COOH and C6H13COO-.
> I do want to know the different behaviours between this two molecules.
> however, I only can get the gro and top files from PRODRG server. I have

What you have here isn't a really difficult molecule, so changing the protonation state of the carboxylic acid to another one (if you already have the other) is not too difficult to do.  For someone starting out, it is certainly not trivial, but it isn't difficult.

Few pointers for you once you have your topology sorted; ensure you add in counter ions for the COO-, background salt may be appropriate or a variable to study, and do the molecules have to be at the two extremes of ionisation or is it only partially ionised?

> an idea is to add H+ ions to the solution and change the pH of this
> solution to push the H+ to the C6H13COO-.

Even if you could add protons to the system (and there was an appropriate forcefield to deal with it, which I am not sure there actually is that you can use with GROMACS), what is the concentration of "H+" in the system at the pH you want things to operate at?  How many atoms does that correspond to in the box size that you are looking at running?

To illustrate why this is an issue, at pH 2 the ratio of H2O molecules to "H+" is approximately 5500 to 1.  That isn't too bad, do able in a reasonable sized water box.  However, it is at more physiological concentrations, say pH 7, then the ratio changes to around 550,000,000 to 1.  That will require a very large system to get a statistically significant number of protons in there.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail. 

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