[gmx-users] exert of special pH

Justin A. Lemkul jalemkul at vt.edu
Sun Dec 20 16:31:40 CET 2009

leila karami wrote:
> Hi
> How I exert my favorite PH in simulation of pr-dna interaction in mdp 
> file? And also special concentration of some salts.

The concept of pH is not one that can be easily defined in a normal MD 
simulation.  Please see the extensive discussion here:


You can, however, assign protonation states to your various amino acids when 
running pdb2gmx.

To alter salt concentration, please see genion -conc.


> Any help will highly appreciated!


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


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