[gmx-users] want to apply electric field in membrane system
sudipta
sudipta.mml at gmail.com
Mon Aug 19 21:15:34 CEST 2013
Thanks for your reply. Is that means my electric field is too high? Should
I reduce the strength of electric field? Which value is suitable for the
electric field? Is my protocol for controlling area and application of
electric field across the membrane fine. By the way I had modeled my
system using MARTINI coarse grain force field with coarse grain polarizable
water molecule.
On Mon, Aug 19, 2013 at 1:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 8/19/13 1:02 PM, sudipta wrote:
>
>> I am coming across the similar problem. In my case I was using
>> semiisotropic pressure and set the compressiblity in x/y as 0.0 to
>> construct the NPAT ensemble. The area in xy plane is not changing but the
>> dimension of z has changed. The system behaves well without the
>> application
>> of electric field of strength 0.5 V/nm. However, the lipid molecules
>> rapidly penetrate (within 5ns period) into the water in presence of that
>> electric field (I think it is rapid electroporation). Basically, after a
>> while it is like a mixture of lipid and water system and the bilayer has
>> destroyed. I don't understand how much logical is it?
>>
>>
> I wouldn't call that electroporation; I'd call it complete destruction of
> the membrane :) Offhand, I seem to recall that electroporation is done
> with a field of somewhere between 1-25 kV/cm, depending on cell type. A
> field of 0.5 V/nm ends up being 5000 kV/cm!
>
> -Justin
>
> These are my keywords
>> Pcoupl = berendsen
>> Pcoupltype = semiisotropic
>> tau_p = 5.0 5.0
>> compressibility = 0.0 3e-4
>> ref_p = 1.0 1.0
>>
>> ;Electric fileld
>> E-z = 1 0.5 0
>>
>>
>>
>>
>> On Mon, Aug 19, 2013 at 8:22 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 8/18/13 11:21 PM, udels can wrote:
>>>
>>> Hi All,
>>>>
>>>> I am facing a strange problem when I was trying to apply electric field
>>>> across a membrane, DMPC, water and ion system. To apply electric field
>>>> across the membrane (in +ve z direction), I had used NPzAT ensemble,
>>>> where
>>>> the Pz is the constant pressure along the z direction and A is the
>>>> constant
>>>> area in xy plane. The following essential keywords were used to
>>>> construct
>>>> such kind of system.
>>>>
>>>> Pcoupltype = anisotropic
>>>> tau_p = 1.0 1.0
>>>> compressibility = 0.0 0.0 3e-4 0.0 0.0 0.0
>>>> ref_p = 0.0 0.0 1.0 0.0 0.0 0.0
>>>>
>>>> ;Electric fileld
>>>> E-z = 1 2.0 0
>>>>
>>>> Here, I had chosen anisotropic coupling and two tau_ps are for two
>>>> groups(DMPC and water_ion). The compressibility for x, y and off
>>>> diagonal
>>>> elements were chosen as 0 and the compressibility in z direction was
>>>> chosen
>>>> as 3e-4. Logically, such compressibility factors ensures that area in xy
>>>> plane will not change.
>>>>
>>>> However, I am not getting the expected results. The strange thing is
>>>> that
>>>> the bilayer and water mixed up, the lengths of box abruptly are changed
>>>> in
>>>> three directions, and the water molecules are arranged in a linear
>>>> fashion
>>>> (I think it is due to the effect of electric field). May be the electric
>>>> field is high enough and as a result the electroporation occurs very
>>>> rapidly. Moreover, the are area in xy plane is not fixed, they are
>>>> changing
>>>> abruptly. I don't understand why does it happen. This is because the
>>>> compressibilities are zero along x and y directions. Another strange
>>>> thing
>>>> is that there are too many LINCS warning. How do I resolve this issue.
>>>> Please help me out in this regard.
>>>>
>>>>
>>>> Does a simulation in the absence of the electric field run normally?
>>> It
>>> sounds like there is something fundamentally wrong, but with so much
>>> going
>>> on it's hard to determine the root cause.
>>>
>>> -Justin
>>>
>>> --
>>> ==============================****====================
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.****edu <jalemkul at outerbanks.**
>>> umaryland.edu <jalemkul at outerbanks.umaryland.edu>> | (410)
>>> 706-7441
>>>
>>> ==============================****====================
>>>
>>>
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> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
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