[gmx-users] Placing ions in the specified positions

James Starlight jmsstarlight at gmail.com
Thu Feb 16 08:13:42 CET 2012

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.


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