[gmx-users] Applying an electric field on lipids
nedomacho at gmail.com
Tue Nov 21 04:39:03 CET 2017
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.
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
> > 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
> >> 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
> >> 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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