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

[anu chandra]

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).
What all modification I should make in mdp input file to take care of the
slab geometry?


Many thanks in advance


Anu

On Tue, Jul 14, 2015 at 3:57 PM, anu chandra <anu80125 at gmail.com> wrote:

> Thanks for the reply Mark. Yes, its a periodic box. Below is the input mdp
> I have used for  minimization.
>
> define                  = -DREST_ON -DSTEP6_0
> integrator              = steep
> emtol                   = 1000.0
> nsteps                  = 5000
> nstlist                 = 10
> cutoff-scheme           = Verlet
> rlist                   = 1.2
> vdwtype                 = Cut-off
> vdw-modifier            = Force-switch
> rvdw_switch             = 1.0
> rvdw                    = 1.2
> coulombtype             = pme
> rcoulomb                = 1.2
> ;
> constraints             = h-bonds
> constraint_algorithm    = LINCS
>
> **************************************************************
>
> Please find attached the snapshot of the system before (initial.png) and
> after minimization (min1.png). Green is the calcium ions and blue is the
> chloride ions. All I have done is adding calcium ions to one side of the
> membrane. It looks to me like calcium ions enetering from the opposite side
> of the box ( ie from its image box). Hope I am taking care of the periodic
> condition. Please have a look and help me to figure out the problem.
>
> On Tue, Jul 14, 2015 at 11:47 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> 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
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