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

[Mark Abraham]

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 <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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>