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.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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