[gmx-users] want to apply electric field in membrane system

Justin Lemkul jalemkul at vt.edu
Mon Aug 19 23:05:14 CEST 2013 


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 <jalemkul at 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 <jalemkul at 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 <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
>>>>>>> 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
>>>>>>
>>>>>> --
>>>>>> ==============================******====================
>>>>>>
>>>>>>
>>>>>>
>>>>>> 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 <jalemkul at outerbanks.**umaryland.edu<jalemkul at outerbanks.umaryland.edu>>>
>>>>>> | (410)
>>>>>> 706-7441
>>>>>>
>>>>>> ==============================******====================
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/******mailman/listinfo/gmx-users<http://lists.gromacs.org/****mailman/listinfo/gmx-users>
>>>>>> <htt**p://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>>>>>>
>>>>>> <htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/**listinfo/gmx-users>
>>>>>> <h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>>   * Please search the archive at http://www.gromacs.org/**
>>>>>> Support/Mailing_Lists/Search<**h**ttp://www.gromacs.org/**Support/**<http://www.gromacs.org/Support/**>
>>>>>>
>>>>>> Mailing_Lists/Search<http://**www.gromacs.org/Support/**
>>>>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>
>>>>>>>> before
>>>>>> posting!
>>>>>>
>>>>>> * Please don't post (un)subscribe requests to the list. Use the www
>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>> * Can't post? Read http://www.gromacs.org/******Support/Mailing_Lists<http://www.gromacs.org/****Support/Mailing_Lists>
>>>>>> <http://**www.gromacs.org/**Support/**Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists>
>>>>>>>
>>>>>> <http://**www.gromacs.org/**Support/**Mailing_Lists<http://www.gromacs.org/Support/**Mailing_Lists>
>>>>>> <http:/**/www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>>>>>>
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>   --
>>>> ==============================****====================
>>>>
>>>> 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 <jalemkul at outerbanks.umaryland.edu>> | (410)
>>>> 706-7441
>>>>
>>>> ==============================****====================
>>>> --
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>>>>
>>>> * Please search the archive at http://www.gromacs.org/**
>>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/**
>>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before
>>>> posting!
>>>> * Please don't post (un)subscribe requests to the list. Use the www
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> * Can't post? Read http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists>
>>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>>>>
>>>>
>>>>
>> --
>> ==============================**====================
>>
>> 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)
>> 706-7441
>>
>> ==============================**====================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>

-- 
==================================================

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 | (410) 706-7441

==================================================

More information about the gromacs.org_gmx-users mailing list