Additionally, what is the difference between the different wall types? They are stated as 9-3, 10-4, and 12-6, but I don't know what is meant by that.
On Tue, Aug 5, 2014 at 1:20 PM, AJ Lanphere <ajlanph...@gmail.com> wrote: > So, I've been looking over the sections on walls in the manual and I have > a few questions on the specifics. > - Do the walls have to be composed of a solid material, or can they be set > as just a boundary? I don't want my glass drifting out of the simulation > box and into space, but I don't want it interacting with an interface, > either. > - Is it possible to remove periodicity from positive Z, but not negative > Z? As in, can I set it up so that I'm only forming an "exposed" surface on > one face of my box, instead of creating effectively a sheet of glass? I'm > concerned that, since my simulation box is only 4.5nm on a side, creating > two surfaces that close together will result in unrealistic structure. > > Thanks, > AJ L > > > On Mon, Jul 21, 2014 at 2:35 PM, David van der Spoel <sp...@xray.bmc.uu.se > > wrote: > >> On 2014-07-21 18:33, AJ Lanphere wrote: >> >>> Hello all, >>> >>> I am using GROMACS to simulate the melting and annealing of glasses. >>> Currently I've been working only with simulations of the glass bulk, with >>> periodic boundaries so the glass is connected on all sides. I was >>> wondering >>> if GROMACS can be used to simulate solid surfaces, because I have not >>> seen >>> any methods for doing so in the manual and a brief literature search has >>> also not returned any useful references. >>> >>> We have done some stuff with glass surfaces: >> David van der Spoel, Erik J. W. Wensink and Alex C. Hoffmann: Lifting a >> glass from a wet table: a microscopic picture Langmuir 22 pp. 5666-5672 >> (2006) >> >> you can also use analytic walls, check the manual. >> >> >> Any advice would be greatly appreciated. >>> >>> Regards, >>> AJ Lanphere >>> >>> Graduate Student Researcher >>> Inamori School of Engineering, Alfred University >>> 1 Saxon Drive, Alfred, NY 14802 >>> >>> >> >> -- >> 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 >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.