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

[朱文鹏]

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?

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>
Subject: Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate
Cc: gmx-users at gromacs.org
Message-ID: <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>>
> 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>>
> Message-ID: <52033C9B.4040806 at xray.bmc.uu.se
> <mailto:52033C9B.4040806 at xray.bmc.uu.se>>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> 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>.
> 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


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