[gmx-users] request

Mark Abraham mark.j.abraham at gmail.com
Tue Dec 5 18:51:55 CET 2017


As the message hints, you previously used mdrun -deffnm and now you are
not, so mdrun does not know whether your intention is to do a new
simulation or continue the old one with the same files.


On Wed, Dec 6, 2017, 2:01 AM <mmahmoudig at razi.tums.ac.ir> wrote:

> whats causes this error?
> Command line:
> gmx mdrun -s md_0_1 -cpi md_0_1.cpt
> Output file appending has been requested,
> but some output files listed in the checkpoint file md_0_1.cpt
> are not present or not named as the output files by the current program:
> Expect output files present:
> Expected output files not present or named differently:
> md_0_1.log
> md_0_1.xtc
> md_0_1.edr
> -------------------------------------------------------
> Program: gmx mdrun, version 2016.3
> Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)
> Fatal error:
> File appending requested, but 3 of the 3 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.
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