[gmx-users] Regarding pH simulation

Justin Lemkul jalemkul at vt.edu
Wed Feb 13 14:24:47 CET 2013

On 2/13/13 8:23 AM, Sathish Kumar wrote:
>    Hai,
>               I want to do simulation of a protein at pH 12.but I was unable
> to do that and I dont know how to set up mdp files for the pH.Can you
> please suggest me how to do.
>                           thank You.

This question gets asked pretty often (hint: check the archives).  The concept 
of pH is ill-defined in a classic MD simulation.  Without the ability to 
actually transfer protons, one approximation you can make is a constant 
protonation state of the solute, which reflects the principal state of each 
titratable group at the desired pH.  All residues with multiple protonation 
states can be set however you like with pdb2gmx.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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