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). Wha

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 wrote: > Dear Gromacs users, > > I am working with

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

Dear Gromacs users, I am working with membrane proteins. The system contains CaCl2 ions and I build the system with calcium ions on one side of the membrane (here, upper layer) and chloride ions distributed on both side of the membrane, in order to maintain the physiological condition. Unfortunat