[gmx-users] want to apply electric field in membrane system
jalemkul at vt.edu
Mon Aug 19 14:22:14 CEST 2013
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 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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