If the system does not explode, everything is correct. Though your solution is perhaps in the wrong place in relation to the tube.
Dr. Vitaly V. Chaban On Tue, Dec 10, 2013 at 10:02 AM, Atila Petrosian <atila.petros...@gmail.com> wrote: > Dear Justin > > > Based on your suggestion, I added C-C bond length to z dimension of box > (before: 5.5 3.5 3.5, now: 5.5 3.5 3.6418). > > Then I used genion to neutralize system using replacing 2 water molecules > by 2 Na ions, gro file obtained from genion is strange. > > When I see this gro file by vmd, some carbon atoms of CNT leave the box. > > Figure is in the bellow link: > > https://www.dropbox.com/s/kt1xk4ps3kbxze3/cnt-pic.docx > > > What is reason of this issue? > > How to fix it? > -- > 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.
