Continuing from extended simulation fails to find output files

GROMACS version: 2019.6
GROMACS modification: No

Dear all,

I have extended my simulation with the following instruction:

  1. gmx convert-tpr -s md_0_1.tpr -extend 50000 -o md_1_2.tpr
  2. gmx mdrun -deffnm md_1_2 -cpi md_0_1.cpt -noappend

It generated a bunch of .part0009 files (edr, trr etc etc)

Now, because the machine is not run 24/7, I have tried to stop and continue with the following command:

gmx mdrun -deffnm md_1_2 -s md_1_2.tpr -cpi md_1_2.cpt -append

Which throws the following error:

Output file appending has been requested,
but some output files listed in the checkpoint file md_1_2.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:

The files are indeed present in the directory, can anyone help out?

I have tried renaming the part0009 files to just md_1_2 to match -deffnm but still throws an error.

Thanks in advance for the help.

Could you paste all your input files?

Hi. I have already complete the simulation. What I did was to continue using the noappend command then merge all the xtc outputs (part0009, part0010…) together at the end of the simulation.

Thanks for trying to help though. I read somewhere by Justin saying that the append function isn’t supposed to be used for continuing an ended simulation. So I’ll just leave that as it is.

I’m facing the same problem can you please help how the problem was solved??

please ASAP

The same happened to me and I solved the problem by using the tag -deffnm

  gmx mdrun -s inputFileName.tpr -cpi inputFileName -deffnm inputFileName

Then GROMACS is able to find the input files and append the output to them
Hope this help

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