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

[Edjan Silva]

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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> >
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> End of gromacs.org_gmx-users Digest, Vol 175, Issue 60
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