[gmx-users] on MD at constant pH

[Mark Abraham]

On 28/03/2012 9:42 PM, Justin A. Lemkul wrote:
>
>
> Acoot Brett wrote:
>>
>> Dear All,
>>
>> Currently is it possible to run MD at a constant pH value?
>>
>
> The concept of pH is not well defined in MD simulations.  In normal 
> MD, you can't transfer protons and you can't explicitly model the 
> actual hydronium concentration without making your box unreasonably 
> large (which also assumes there are parameters in your chosen force 
> field for H3O+).
>
> There are, of course, constant pH methods, but they are not 
> implemented in Gromacs.  There is extensive discussion of these topics 
> in the list archive.

...and at 
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation

Mark

>
>
> At present, you can model a constant protonation state of your 
> molecule.  You should not, of course, equate this with a true 
> "constant pH," but the model is often used.  You can assign your 
> molecule the predominant protonation state at a given pH.
>
> -Justin
>