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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
