[gmx-users] MD simulation with varying pH

[Mark Abraham]

On 07/05/2012 05:03 PM, J Peterson wrote:
> Dear GROMACS Users,
>
> I'm planning to work on a protein that activates itself under lower pH
> conditions. And I don't have any clues how to do it in GROMACS. My first
> question is about the possibilities to do this in GROMACS, has anyone done
> this before? It can even be a constant simulations at a particular
> lower/higher pH or gradually lowering/increasing pH.
>
> Any suggestion on this would give me a lead.

http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation 
discussing various basic issues here.

Mark