Re: [gmx-users] Placing ions in the specified positions
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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Placing ions in the specified positions
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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Placing ions in the specified positions
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 -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
