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

Mark Abraham Mark.Abraham at anu.edu.au
Sat May 23 08:32:18 CEST 2009

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 

> 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 :-)


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