[gmx-users] Placing ions in the specified positions

Peter C. Lai pcl at uab.edu
Thu Feb 16 09:09:20 CET 2012

With xyz periodic boundary conditions, the ions will eventually appear as if 
they are diffusing into the extracellular compartment from above as they 
diffuse down the -Z and leave the original box, anyway. So unless you actually
need them *only interacting* with the intracellular side by using walls, it 
doesn't really matter where the ions are placed as long as they aren't stuck 
somewhere illogical (e.g. inside the bilayer)

On 2012-02-16 10:13:42AM +0300, 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.
> Thanks
> James

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Peter C. Lai			| University of Alabama-Birmingham
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