[gmx-users] Applying an electric field on lipids

[Sithara Perera]

The .mdp file parameter for electric field is as follows.

E_z        = 1    -0.7    1    ; electric field

I want to stop the movement of bi-layer along the z axis as the hypothesis
is to check whether a super charge protein can dislocate the DPPC bi-layer
under an electric field.
Correction, the electric field applied is 0.7V/nm



On Tue, Nov 21, 2017 at 9:08 AM, Alex <nedomacho at gmail.com> wrote:

> I've never worked with CG models, but I assume that the lipid structure is
> well-represented and electrically neutral. That said, uncompensated
> momentum in all MD simulations can arise when a high driving field is
> applied suddenly instead of a ramp. When you say that your field is
> -0.7mV/nm,
> does this mean that it's something like "E-z                 = 1 -0.0007
> 0.0
> " in your mdp file? The units are V/nm, not mV/nm.
>
> Alex
>
> On Mon, Nov 20, 2017 at 6:15 PM, Sithara Perera <
> sithara.perera1993 at gmail.com> wrote:
>
> > Yes. The system was stable and simulations showed that the bi-layer is
> > before applying an electric field.
> >
> > On Tue, Nov 21, 2017 at 1:59 AM, Alex <nedomacho at gmail.com> wrote:
> >
> > > Do you precede your production simulation with a relaxation run without
> > an
> > > electric field?
> > >
> > > Alex
> > >
> > >
> > >
> > > On 11/20/2017 12:16 PM, Sithara Perera wrote:
> > >
> > >> Dear gmx-users,
> > >>
> > >> I'm doing molecular dynamic simulations of protein interaction with
> > lipid
> > >> bi layers using CGmartini force fields under an electric field.
> > >>
> > >> But when I apply the electric field and simulated for 50 ns under
> > >> -0.7mV/nm, the bi layer moves in the electric field and then
> eventually
> > >> reaches the bottom of simulation box. So it is not possible to see the
> > >> protein interaction with the bi layer. I tried applying position
> > restrains
> > >> on z axis, but then the box dimensions started to change
> > >>
> > >> The bi layer a 512DPPC bi layer.
> > >> What can I do to fix this??
> > >>
> > >>
> > >>
> > >> ---------
> > >> Sithara Perera
> > >> USJP
> > >>
> > >
> > > --
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