Hi, You can use packmol to generate your initial configuration.
On Fri, May 15, 2015 at 7:56 PM, Alex <nedoma...@gmail.com> wrote: > Hi, > > I am not sure anyone will be able to help, because this isn't really about > Gromacs. Can you please clarify who "they" are and what exactly you mean by > "perpendicular" when talking about surfactants? Also, what are those > surfactants? Anyway, a reference to a representative paper and some > instructions on where to quickly see what you're talking about would be > nice. Once again, this isn't something Gromacs-specific. > > Alex > On May 15, 2015 9:17 AM, "Golnaz Roudsari" <golnaz.c...@gmail.com> wrote: > > > Dear gmx-user > > I want to simulate graphene and surfactants in water. In most of the > paper > > they put surfactants perpendicular on the graphene sheet. I have problem > in > > initial configuration. I do not know how They put them perpendicular on > the > > graphene sheet. I can not put them random in my box because I do not > have a > > perfect system for more than 50 ns MD run. > > Thank you in advance > > Golnaz Vahabpour > > -- > > 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. > -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- 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.