On 8/19/13 4:56 PM, sudipta wrote:
Basically, few litterateurs suggested that the electric field generates a
stable water pore inside a membrane. I am motivated by that fact and try to
create a water pore for my system.
I found few litterateurs on this topic. However, I am based on a protocol
as suggested by Marrinik et al (plos computational biology, 6, e1000810,
2010). Although, they used octane slab instead of using lipid in their
first setup. Interestingly, they showed the electroporation of octane
occurs within very short period (600 ps) when they applied electric field
of strength 0.8V/nm. So, is it really electroporation or just destruction
of octane layer. I am really confused from their information.
What they report certainly looks like a discrete pore being formed. What you
described didn't seem like the same thing, but maybe that's just a
miscommunication. I am surprised by the magnitude of the field, though. Maybe
the size of the system has an effect; it's not something I have personally tried.
In their real membrane system (they used DMPC), they considered a double
bilayer setup and created an electric field by transmembrane ionic charge
imbalance. By that way they created an electric field of strength 0.7 V/nm
across the membrane. In another setup, they just directly applied an
electric field of strength 0.3-0.7 V/nm. However, when I am applying an
electric field of strength 0.5 V/nm across the membrane directly, the
bilayer destroys. Do you have any idea what is going on in my system? Any
suggestion will be appreciated.
I would suggest trying to reproduce their protocol exactly. If you can't,
request input files directly from the authors.
-Justin
On Mon, Aug 19, 2013 at 4:11 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 8/19/13 3:15 PM, sudipta wrote:
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
The answers here all depend on what you're trying to observe, but it
sounds to me like all you're accomplishing is frying the membrane. I doubt
that's useful.
electric field across the membrane fine. By the way I had modeled my
Maybe. What does an analysis of published literature suggest?
-Justin
system using MARTINI coarse grain force field with coarse grain
polarizable
water molecule.
On Mon, Aug 19, 2013 at 1:51 PM, Justin Lemkul <jalem...@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 <jalem...@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
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Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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