[gmx-users] Error in md simulation

[Mark Abraham]

Hi,

I can't tell whether your system preparation workflow has a relevant error,
neither can grompp, which is why it is suggesting that you consider whether
you have a problem. If the atoms are differently ordered between the two
files, then that's definitely a problem.

You say the atom names match, but without e.g. the grompp command, and its
output and being able to see the files that were actually used in the
command, nobody can comment. My guess is that you are not comparing the
same files that you are passing to grompp, or that the tool is right and
e.g. some names are too long to fit in fixed-width fields of your .gro
structure file.

Mark

On Thu, May 31, 2018 at 9:52 AM Gonzalez Fernandez, Cristina <
cristina.gonzalezfdez at unican.es> wrote:

> Hi Mark,
>
> I don't have found any message about this error. Maybe someone asked about
> it but I don't found it, this is why I have asked.
> Do you know how to solve my question?
>
> Best,
> C.
>
> -----Mensaje original-----
> De: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] En nombre de Mark
> Abraham
> Enviado el: jueves, 31 de mayo de 2018 9:35
> Para: gmx-users at gromacs.org
> CC: gromacs.org_gmx-users at maillist.sys.kth.se
> Asunto: Re: [gmx-users] Error in md simulation
>
> Hi,
>
> Isn't there earlier messages telling you which atoms and names don't match?
>
> Mark
>
> On Thu, May 31, 2018 at 9:28 AM Gonzalez Fernandez, Cristina <
> cristina.gonzalezfdez at unican.es> wrote:
>
> > Dear Gromacs users,
> >
> >
> > I am trying to perform a simulation, and this error apperars:
> > "131 non-matching atom names. Atom names from .top will be used, atom
> > names from .gro will be ignored"
> >
> > However, I have checked the name of the atoms (atom column) in [atoms]
> > of .top and they are the same as the atoms name in  the second column
> > of the .gro file.
> > Does anyone know how to solve it?
> >
> >
> > Any help will highly been appreciated.
> >
> >
> >
> > Best,
> >
> >
> >
> > C.
> >
> > --
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