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 <sp...@xray.bmc.uu.se > <mailto:sp...@xray.bmc.uu.se>> > Subject: Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate > To: Discussion list for GROMACS users <gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org>> > Message-ID: <52033c9b.4040...@xray.bmc.uu.se > <mailto:52033c9b.4040...@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>. > sp...@xray.bmc.uu.se > <mailto:sp...@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. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists