[gmx-users] want to apply electric field in membrane system
jalemkul at vt.edu
Mon Aug 19 19:51:38 CEST 2013
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!
> 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
>>> 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
>>> 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
>>> (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
>>> 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 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)
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Justin A. Lemkul, Ph.D.
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 | (410) 706-7441
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