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

朱文鹏 jasonzhu925 at gmail.com
Thu Aug 8 13:17:37 CEST 2013

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?

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.


--- original message ---------------------------

Message: 1
Date: Thu, 08 Aug 2013 08:37:15 +0200
From: David van der Spoel <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>
Message-ID: <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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se


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