[gmx-users] Can't observe ion separation under the influence of electric field

[Live King]

Dear David and Harutyun,

Thanks for your reply. Density plots were the first check I did. They show
a very minor difference. I imagined that the electric field is not
sufficient, however,  presence of high electric field ( > 1 V or 1000mV)*
disrupts the membrane and my simulation crashes*. Is there any solution to
this problem? I will have a look at compel.

On Thu, Feb 13, 2020 at 6:21 PM Harutyun Sahakyan <h_sahakyan at mb.sci.am>
wrote:

> You can use compel and build a double bilayer system to separate ions.
> However, if you separate positive and negative ions, you will have very
> high membrane potential, event two ions difference can raise potential
> about 200 mV. In your case, I suppose 500 mV is not enough to separate all
> ions in a PBC box.
>
> https://www.mpibpc.mpg.de/grubmueller/compel
>
>
>
> Harutyun Sahakyan
> Senior Assistant at Laboratory of
> Computational Modeling of Biological Processes,
> Institute of Molecular Biology, NAS, Armenia, Yerevan
> Tel: +374 93 323990
> h_sahakyan at mb.sci.am
> sahakyanhk at gmail.com
>
> February 13, 2020 2:07 AM, "Live King" <vikasdubey1008 at gmail.com> wrote:
>
> > Dear all,
> >
> > I am running a simple test case with a lipid bilayer (DMPC), water, and
> > ions (150mM KCL) under the influence of a constant electric field (
> 300mV,
> > 500mV, and 700mV). *I expected positive and negative ions to separate in
> > the presence of an external electric field*. However, I am not observing
> > such behavior despite running the all-atom simulation for 400ns in any
> > case. I am using gromacs 2018.2, my mdp file is standard charmm-gui
> > production with electric field option.
> >
> > for example 500mV electric field in Z-direction :
> > electric-field-z = 0.060 0 0 0 ; *500**mv = 8.25nm* 0.060 =
> > 500 mV *
> >
> > Are there any settings to run the electric field simulation that I miss?
> > Any help will be greatly appreciated.
> >
> > Thank you,
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