On Jan 26, 2014 9:30 AM, "Mahboobeh Eslami" <mahboobeh.esl...@yahoo.com> wrote: > > hi GMX users > i simulate protein ligand complex in dodecahedron box > when i use following command > > editconf -f complex.pdb -o newbox.gro -bt dodecahedron -d 1.0 -c > My complex is not located in the center of box, > > How do I put the complex in the center of box?
It is in the center of the dodecahedral cell, but not in the triclinic representation of that cell, which is the default output representation. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditionsfor info and suggestions on using trjconv to get the visual confirmation you seek. Mark > thanks for your's help > -- > 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.
