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

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 29 05:11:57 CET 2011

cuong nguyen wrote:
> Dear Justin,
> 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 
> an idea is to add H+ ions to the solution and change the pH of this 
> solution to push the H+ to the C6H13COO-.

I sincerely doubt that any classical molecular mechanics force field can achieve 
this.  Bonds cannot be broken or formed without QM/MM, which is not feasible for 
a system of more than a few dozen (maybe a hundred) atoms.  There are titration 
MD algorithms that exist, but they are not available in Gromacs yet.

> I have received your response about the FAQ of PRODRG and try to find 
> out the solution. However, I just started using GROMACS 2 months ago and 
> my english is not good enough. So I have not known how to get the gro 
> and top files of C6H13COOH yet.

You need to run PRODRG once to get the atom names that the server uses, then run 
it again by providing the ADDHYD or DELHYD keywords for the atom that you want 
(de)protonated.  I think an example is provided online.



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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