it's hard to say without knowing how you prepared and relaxed your micelle before adding water, so I can only provide you a few general comments:
(1) a properly relaxed, well-packed micelle should not present any voids and water should not go inside the micelle (check the literature, this has already been done a number of times already for SDS and other surfactants) (2) increasing the value for -vdwd should decrease the number of water molecules inside the micelle, even if the preparation step was not accomplished so carefully. (3) maybe you could try Packmol: http://www.ime.unicamp.br/~martinez/packmol/ On Mon, Dec 29, 2014 at 5:39 AM, Mina Hashemi <hashemi.mi...@gmail.com> wrote: > Dear gromacs users > > I prepared my simulation system containing SDS. > > Then I added water molecules using genbox. Some water molecules > entered in to the micelle. > > How to remove water molecules inside the micelle? > > Any help will highly appreciated. > -- > 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. > > -- _____________ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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.