Hi, Element, as in small thing from which bigger things are made. See http://www.gromacs.org/Documentation/Errors#Atom_index_(1)_in_bonds_out_of_bounds
Mark On Sun, Jan 21, 2018, 01:26 حلیمه میرسالاری <h.mirsalar...@gmail.com> wrote: > Hi > order of element? > > > 2018-01-20 15:59 GMT-08:00 Mark Abraham <mark.j.abra...@gmail.com>: > > > Hi, > > > > Like the message says, you have mishandled the order of the elements of > > your topology. Look at the examples in the documentation. > > > > Mark > > > > On Sun, Jan 21, 2018, 00:40 حلیمه میرسالاری <h.mirsalar...@gmail.com> > > wrote: > > > > > Dear all > > > > > > l am using gromacs 4.5.5 version for simulation carbon nanotubes in > tip3p > > > water with charmm27 force feild. > > > I used grompp for energy minmization,but l encountered with > > > fatal error: > > > > > > [ file tip3p.itp, line 40]: > > > Atom index (1) in settles out of bounds (1-0). > > > This probably means that you have inserted topology section "settles" > > > in a part belonging to a different molecule than you intended to. > > > In that case move the "settles" section to the right molecule. > > > > > > Thanks a lot > > > -- > > > 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. > -- > 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.
