[gmx-users] How to solve this fatal error?

[Mark Abraham]

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.mirsalari66 at gmail.com> wrote:

> Hi
> order of element?
>
>
> 2018-01-20 15:59 GMT-08:00 Mark Abraham <mark.j.abraham at 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.mirsalari66 at 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-request at 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-request at 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-request at gromacs.org.