[gmx-users] on MD at constant pH
Mark.Abraham at anu.edu.au
Wed Mar 28 13:52:03 CEST 2012
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.
> 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.
More information about the gromacs.org_gmx-users