[gmx-users] Charge neutralization

Mark Abraham Mark.Abraham at anu.edu.au
Thu Dec 10 07:45:01 CET 2009

Arden Perkins wrote:
> Hey all, I am trying to examine couplings between Mg+2 ions and a 
> peptide with a -5 charge. I would like to optimize couplings and have 
> considered using a +1 charge from the system. I read that GROMACS can do 
> this and that in theory it should have the same effect as adding ions 
> but it is not standard practice. For future simulations I plan to 
> increase the [Mg+2] and am worried about couplings from Cl- if I were to 
> use Cl- to neutralize the excess positive charge. Is it ok to use the 
> system to neutralize these charges? Or is that considered a bad 
> experimental design?

What do you mean by using "the system to neutralize these charges"?


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