So, you have a charged protein under a high electric field, moving and
bumping into an unrestrained lipid bilayer. Maybe use position
restraints, those are well documented in the Gromacs manual.
Alex
On 11/20/2017 11:23 PM, Sithara Perera wrote:
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 <nedoma...@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.perera1...@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 <nedoma...@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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