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

Mark Abraham mark.j.abraham at gmail.com
Tue Jul 14 12:47:32 CEST 2015


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.


On Tue, Jul 14, 2015 at 12:42 PM anu chandra <anu80125 at gmail.com> wrote:

> 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. Unfortunately, after the very
> first minimization, when I visualize the gro file in VMD I have noticed
> that  the calcium ions  entered the opposite side of the membrane (ie,
> lower layer) and subsequently get distributed in the lower layer during the
> equilibration process. Though I have tried with varying Z-dimension values
> of the box size, the same has been noticed when visualizing the output gro
> file with VMD.
> Please help me to figure out what is wrong with my simulation box.
> Many thanks
> Anu
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