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

[David van der Spoel]

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>>
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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>.
> 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