[gmx-users] Placing ions in the specified positions

[Mark Abraham]

On 16/02/2012 6:13 PM, James Starlight wrote:
> Dear Gromacs users!
>
>
> I've constructed my biphastic system with the water-ccl4-water layers 
> where in the ccl4 layer I've placed my membrane protein.
>
> Now I'd like to place addition 5 Cl ions to the bottow leafleat of 
> water to mimick the 'positive-inside rule' (my protein consist of 5 
> Lys) of the membrane protein topology. How I could specify to place 
> some ions in the desired possitions? As i understood the genion place 
> ions in the random possitions so I've obtained 3 ions in the bottom 
> and 2 in the upper layer.

Make five holes by removing cunningly chosen water molecules reasonably 
spaced out. Add five plus a few extra Cl ions, and remove those that 
went to unsuitable locations. Equilibrate forever - but you were going 
to have to do this anyway!

Mark