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
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