[gmx-users] Placing ions in the specified positions
Mark.Abraham at anu.edu.au
Thu Feb 16 08:58:27 CET 2012
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!
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