[gmx-users] Regarding extending simulations

Mark Abraham mark.j.abraham at gmail.com
Tue Mar 21 10:01:08 CET 2017


Your first run used gmx mdrun -deffnm, and like the error message says, the
checkpoint file knows what the output filenames were in that case. But your
second mdrun doesn't specify -deffnm, so mdrun doesn't know whether you
meant to append to the old files, or not provide that checkpoint file, or
not append, or what. If you want to append to the old files, because the
run is logically equivalent to a single long run (which is a judgement you
can make, and mdrun should not make for you), then like the message
suggests, use -deffnm the same way you did the first time. Now mdrun knows
what output files you meant it to use, and that matches the checkpoint file
you gave, and so mdrun knows how to implement the default approach of file
appending. Alternatively, you can turn appending off, as the message


On Tue, Mar 21, 2017 at 5:39 AM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> Hello,
> I ran a md run of 20ns [10000000*.002] and i got the files as md.edr,
> md.log, md.tpr, md.gro, md.xtc, md.cpt etc.,
> Now i want to extend/continue my simulation from 20 ns to again 20 ns
> (total 40 ns).
> So i gave the command as -
> gmx convert-tpr -s md.tpr - extend 20000 -o md1.tpr
> gmx mdrun -v -s md1.tpr -cpi md.cpt -append
> But i am getting the following errors..
> Output file appending has been requested,
> but some output files listed in the checkpoint file md.cpt
> are not present or not named as the output files by the current program:
> Expect output files present:
>   md.log
> Expected output files not present or named differently:
>   md.xtc
>   md.trr
>   md.edr
> -------------------------------------------------------
> Program:     gmx mdrun, version 2016.2
> Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)
> Fatal error:
> File appending requested, but 3 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.
> why is this error coming in spite i have all the above files in my workin
> directory and i have not changed any names neither have edited any of
> those....
> --
> With Best Regards,
> Research Scholar,
> Department of Chemistry, NITK.
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