[gmx-users] want to apply electric field in membrane system
udelcan1 at gmail.com
Mon Aug 19 05:21:16 CEST 2013
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
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.
Thanks in advance
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