[gmx-users] Recovery simulation error

Bratin Kumar Das 177cy500.bratin at nitk.edu.in
Sat Nov 17 04:57:06 CET 2018

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
> --
> *Estudiante Doctorado en Biotecnología*
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