[gmx-users] Lipid Bilayer on the Graphene or GO substrate

[David van der Spoel]

On 2013-08-09 14:29, 朱文鹏 wrote:
> Hello David,
> 
> Thank you again for your reply. It is very interesting idea.
> 
> Do you mean I can using a grand canonical ensemble to control the 
> surface tension of lipid bilayer by varying its number during my 
> simulations? Is there an existing method in Gromacs to implement so? Or 
> I need to modify the Gromacs code? Could you please give me a clue?

No this isn't implemented and will be quite hard to do.
Why don't you try to make a monolayer of the right size using e.g.
http://www.membuilder.org and the place this on the graphene using a
text editor. Then if you have the right density and you solvate the
layer it will stay a monolayer. In principle you could also put a
mixture of lipids and water in the box and it will assemble after a
while into a monolayer.

I guess you want a monolayer, not a bilayer, and hence you will have to
remove one of the two generated layers.

> 
> And I tried to "jump lipids" on the 2D periodic graphene layer by adding 
> lipids continuously. Due to the hydrophobicity of lipid tails, the added 
> lipid tails tend to be attached on the graphene layer and form a planar 
> monolayer. But it is not the lipid bilayer I am concerned. If I directly 
> put a periodic lipid bilayer onto the 2D periodic graphene layer, the 
> water molecules between them have no pathway to escape outside. The 
> water permeability through the bilayer is slow in the timescale of 
> MD simulations. The system seems to be time-consuming to find the 
> equilibrium distance between the periodic graphene and the periodic 
> lipid bilayer in MD simulations.
> 
> Best,
> Jason
> 
> ------- original message---------------------
> 
> Message: 2
> Date: Thu, 08 Aug 2013 13:41:59 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se 
> <mailto:spoel at xray.bmc.uu.se>>
> Subject: Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate
> Cc: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Message-ID: <52038407.7000904 at xray.bmc.uu.se 
> <mailto:52038407.7000904 at xray.bmc.uu.se>>
> Content-Type: text/plain; charset=GB2312
> 
> On 2013-08-08 13:17, 朱文鹏 wrote:
>> Hello David,
>>
>> Thank you for your response.
>>
>> Do you mean a finite lipid bilayer on a periodic infinite graphene
>> layer, or a lipid liposome (or a whole spherical cell) on a periodic
>> infinite graphene layer?
> A 2D periodic graphene layer - which will be an infinite molecule, and
> then just dump lipids on them, which will form a periodic monolayer.
> 
> You control the surface tension of the lipids by varying the number. How
> you would compute the surface tension then is another problem.
> 
>>
>> For the first case, how do you control the surface tension of lipid
>> bilayer? For the second case, I cannot set up a very large spherical
>> cell due to the computational cost. If it is too small, it will be
>> different from the actual situation.
>>
>> Best,
>> Jason
>>
>> --- original message
>> -------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 08 Aug 2013 08:37:15 +0200
>> From: David van der Spoel <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>>
>> Subject: Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>>
>> Message-ID: <52033C9B.4040806 at xray.bmc.uu.se <mailto:52033C9B.4040806 at xray.bmc.uu.se>
>> <mailto:52033C9B.4040806 at xray.bmc.uu.se <mailto:52033C9B.4040806 at xray.bmc.uu.se>>>
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>>
>> On 2013-08-07 22:50, 朱文鹏 wrote:
>>> Dear all,
>>>
>>> I am trying to set up an all-atom MD simulation to investigate the
>>> interaction between lipid bilayer and infinite substrate of graphene or
>>> graphene oxide. The edge effects of graphene and graphene oxide are not
>>> what I am concerned. The lipid bilayer is placed on the
>>> substrate parallelly in the x-y direction.
>>>
>>> I know the pressure coupling method of "surface-tension" can control the
>>> surface tension in the x-y plane. But it is only for the whole system. The
>>> lipid layer and graphene substrate are both infinite in the x-y direction.
>>> Can I control the pressure of lipid bilayer and infinite substrate
>>> separately? Otherwise, should I change the lipid bilayer to a finite one
>>> but still with zero surface tension, or change the graphene substrate to a
>>> finite one but without edge effects?
>>>
>>> How can I remove the edge effects from a finite graphene or GO layer? Do
>>> you have any suggestions? I will very appreciate that. Looking forwards to
>>> your reply.
>>
>> Why not make a periodic graphene layer (you will have to generate the
>> topology yourself)? You can put anything you like on top of it, and the
>> have pressure coupling only in the normal direction.
>>>
>>> Best,
>>> Jason
>>>
>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205 <tel:%2B46184714205> <tel:%2B46184714205>.
>>spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>> <mailto:spoel at xray.bmc.uu.se 
> <mailto:spoel at xray.bmc.uu.se>>http://folding.bmc.uu.se 
> <http://folding.bmc.uu.se/>
>> <http://folding.bmc.uu.se/>
>>
>>
>> ------------------------------
> 
> 
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205 <tel:%2B46184714205>.
> spoel at xray.bmc.uu.se 
> <mailto:spoel at xray.bmc.uu.se>http://folding.bmc.uu.se 
> <http://folding.bmc.uu.se/>
> 
> 
> ------------------------------


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se