[gmx-users] Applying an electric field on lipids

[Alex]

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 <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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