[gmx-users] Recovery simulation error (Bratin Kumar Das)

[Mario Andres Rodriguez Pineda]

Thank you very much to all.
Your indications helped me to continue and not lose the work done

Em dom, 18 de nov de 2018 às 14:00, Edjan Silva <edjan.silva at esenfar.ufal.br>
escreveu:

> to the end of the command you typed add: -deffnm cbd211_md
>
>
> Em sáb, 17 de nov de 2018 às 08:00,
> <gromacs.org_gmx-users-request at maillist.
> sys.kth.se> escreveu:
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> >    1. Re: Recovery simulation error (Bratin Kumar Das)
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> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Sat, 17 Nov 2018 09:33:24 +0530
> > From: Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Recovery simulation error
> > Message-ID:
> >         <
> > CAM7TW5tJYoUDJqAPCGEb6oDi58VH-2q_-YmstZoTeNG_aSpmCQ at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Use the following command...
> > Gmx mdrun -v -s cbd211_md.tpr -cpi cbd211_md.cpt -append -deffnm
> cbd211_md
> >
> > On Sat, Nov 17, 2018, 9:26 AM Bratin Kumar Das <
> > 177cy500.bratin at nitk.edu.in>
> > wrote:
> >
> > > Use -deffnm flag and specify the name ..same as the previous output
> > > file...do not forget to give the -append flag
> > >
> > > On Sat, Nov 17, 2018, 3:09 AM Mario Andres Rodriguez Pineda <
> > > mandres at iq.usp.br> wrote:
> > >
> > >> Hi Gromacs Users.
> > >> I has been a simulation with gromacs 2016 but my simulation stopped by
> > an
> > >> energy break. i try to restar in the last checkpoint but this does
> work
> > >> and
> > >> send me this error:
> > >> Expected output files not present or named differently:
> > >>   cbd211_md.log
> > >>   cbd211_md.xtc
> > >>   cbd211_md.trr
> > >>   cbd211_md.edr
> > >> Fatal error:
> > >> File appending requested, but 4 of the 4 output files are not present
> or
> > >> are
> > >> named differently. For safety reasons, GROMACS-2016 and later only
> > allows
> > >> file
> > >> appending to be used when all files have the same names as they had in
> > the
> > >> original run. Checkpointing is merely intended for plain continuation
> of
> > >> runs.
> > >> For safety reasons you must specify all file names (e.g. with
> -deffnm),
> > >> and
> > >> all these files must match the names used in the run prior to
> > >> checkpointing
> > >> since we will append to them by default. If the files are not
> available,
> > >> you
> > >> can add the -noappend flag to mdrun and write separate new parts. For
> > mere
> > >> concatenation of files, you should use the gmx trjcat tool instead.
> > >>
> > >> I used this command:
> > >> gmx mdrun -s cbd211_md.tpr -cpi cbd211_md.cpt -v
> > >>
> > >> All the archives ar in the directory....
> > >>
> > >> Can you help me? Thanks
> > >>
> > >>
> > >>
> > >> --
> > >> *MSc. MARIO ANDR?S RODR?GUEZ PINEDA*
> > >> *Estudiante Doctorado en Biotecnolog?a*
> > >> *UNAL- MEDELL?N *
> > >> --
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-- 
*MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA*
*Estudiante Doctorado en Biotecnología*
*UNAL- MEDELLÍN *