[gmx-users] want to apply electric field in membrane system
sudipta.mml at gmail.com
Mon Aug 19 19:02:23 CEST 2013
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?
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
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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