[gmx-users] genion

[Mark Abraham]

Tamas Horvath wrote:
> I have a protein in water system. The protein has some charge, which I 
> want to neutralise, introducing stochastic ammount of K+ or Cl-. As far 
> as I figured out, the best way to do it is to use genion. Only I don't 
> know beforehand what the protein's charge would be, so I'm wondering if 
> it's possible to tell genion to neutralise the system?

Not knowing the pattern of charge distribution in your protein, and thus 
the net charge, sounds to me like a great way to run the risk of doing 
some worthless simulations and/or bogus science for want of a few 
minutes of observation and thought. I'd call the gromacs utility 
programs' inability to automatically neutralise a system a feature, not 
a bug!

Cheers,

Mark Abraham