[gmx-users] exert of special pH

[Justin A. Lemkul]

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:

http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation

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

To alter salt concentration, please see genion -conc.

-Justin

>  
> 
> Any help will highly appreciated!
> 
>  
> 

-- 
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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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