[gmx-users] How to choose the counter ions for proteins?

[Mark Abraham]

Chih-Ying Lin wrote:
> Hi
> How to choose the counter ions for proteins?

That depends what kind of system you're trying to model. Cellular 
cytoplasm might have different ionic mixes from nerve synapses from agar 
plates.

> Proteins are made of amino acids.
> Does it mean the counter ions of protein H+ or OH-?

It's instructive to calculate the ionic concentration of such ions at 
biochemically relevant pH values and then to determine how many such 
ions might be present in a typical MD simulation cell.

> I think => H+ and OH- ions are not available for the gromos force field, right?
> But, later version 4.0.2 ; they might be available, right?

That's what reading literature is for :-)

Mark