On 2013-08-09 14:29, 朱文鹏 wrote: > 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?
No this isn't implemented and will be quite hard to do. Why don't you try to make a monolayer of the right size using e.g. http://www.membuilder.org and the place this on the graphene using a text editor. Then if you have the right density and you solvate the layer it will stay a monolayer. In principle you could also put a mixture of lipids and water in the box and it will assemble after a while into a monolayer. I guess you want a monolayer, not a bilayer, and hence you will have to remove one of the two generated layers. > > 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 <sp...@xray.bmc.uu.se > <mailto:sp...@xray.bmc.uu.se>> > Subject: Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate > Cc: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> > Message-ID: <52038407.7000...@xray.bmc.uu.se > <mailto:52038407.7000...@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 <sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> >> <mailto: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> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>> >> Message-ID: <52033c9b.4040...@xray.bmc.uu.se >> <mailto:52033c9b.4040...@xray.bmc.uu.se> >> <mailto: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> >> <tel:%2B46184714205>. >>sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> >> <mailto:sp...@xray.bmc.uu.se > <mailto:sp...@xray.bmc.uu.se>>http://folding.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 <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
