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

[David van der Spoel]

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