Re: [gmx-users] Ions moving to the opposite layer during minimization.

Hi, It's a periodic box, right? There is only one water region. You can't get steady-state non-equilibrium ion distribution without forcing it, e.g. https://www.mpibpc.mpg.de/grubmueller/compel Mark On Tue, Jul 14, 2015 at 12:42 PM anu chandra anu80...@gmail.com wrote: Dear Gromacs users, I

Re: [gmx-users] Ions moving to the opposite layer during minimization.

Hi, It looks like the the problem is the asymmetry in ion distribution. I have seen from the literature that such ion asymmetry can be maintain by implementing slab geometry. Can anybody provide me some information of how to build vacuum slab above and below the membrane ( ie in Z direction).