# Mdrun cannot find pullf and pullx files during checkpointed restart

**URL:** <https://gromacs.bioexcel.eu/t/mdrun-cannot-find-pullf-and-pullx-files-during-checkpointed-restart/4707>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [August 31, 2022, 2:33am UTC](https://gromacs.bioexcel.eu/t/mdrun-cannot-find-pullf-and-pullx-files-during-checkpointed-restart/4707 "2022-08-31T02:33:52Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![plagueis](https://avatars.discourse-cdn.com/v4/letter/p/3be4f8/32.png) [@plagueis](https://gromacs.bioexcel.eu/u/plagueis)\
**Post date:** [August 31, 2022, 2:33am UTC](https://gromacs.bioexcel.eu/t/mdrun-cannot-find-pullf-and-pullx-files-during-checkpointed-restart/4707/1 "2022-08-31T02:33:52Z")

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GROMACS version: 2020.6  
GROMACS modification: No

I’m trying to restart a simulation which crashed last night from the checkpoint file, using the usual -cpi checkpoint.cpt with deffnm as usual, but mdrun throws the following error:

> Inconsistency in user input:  
> Some output files listed in the checkpoint file step7\_1ra.cpt are not present  
> or not named as the output files by the current program:)Expected output files  
> that are present:  
> step7\_1ra.log  
> step7\_1ra.trr  
> step7\_1ra.edr
> 
> Expected output files that are not present or named differently:  
> step7\_1ra\_pullx.xvg  
> step7\_1ra\_pullf.xvg  
> To keep your simulation files safe, this simulation will not restart. Either  
> name your  
> output files exactly the same as the previous simulation part (e.g. with  
> -deffnm), or  
> make sure all the output files are present (e.g. run from the same directory  
> as the  
> previous simulation part), or instruct mdrun to write new output files with  
> mdrun -noappend.

However, these files _are_ indeed present and in the same directory, and I _am_ using deffnm at all times!

I don’t care what happens to these files, I’m only using the pull code to enforce a protein-ligand restraint.

I also don’t want to start writing new output files and create a mess that I will have to piece back together.

What can I do?

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**Author:** ![Carsten](https://avatars.discourse-cdn.com/v4/letter/c/f14d63/32.png) [@Carsten](https://gromacs.bioexcel.eu/u/Carsten)\
**Post date:** [August 31, 2022, 2:17pm UTC](https://gromacs.bioexcel.eu/t/mdrun-cannot-find-pullf-and-pullx-files-during-checkpointed-restart/4707/2 "2022-08-31T14:17:44Z")

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Hi,

The error message is a bit misleading here. Unfortunately the `-deffnm` functionality does not work well if you have multiple output files with the same suffix (in your case you have two `.xvg` files). Due to that, you cannot append to your files any more (I suspect the reason is that in the checkpoint file only the default file names are stored, as `_pullx` and `_pullf` are appended later to the filenames).

But if you don’t mind to redo the first part of your calculation: list the filenames for both `.xvg` output files **explicitly** on the command line, so the `.cpt` file directly gets the correct filenames and appending will work later:

`mdrun -deffnm step7_1ra -px step7_1ra_pullx.xvg -pf step7_1ra_pullf.xvg`

BTW it does not matter how your `.xvg` files are called here, just give them different names explicitly with `-px` and `-pf` on the command line.

That should do the trick!

Best,  
Carsten

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<div class="post-metadata">

**Author:** ![plagueis](https://avatars.discourse-cdn.com/v4/letter/p/3be4f8/32.png) [@plagueis](https://gromacs.bioexcel.eu/u/plagueis)\
**Post date:** [August 31, 2022, 2:33pm UTC](https://gromacs.bioexcel.eu/t/mdrun-cannot-find-pullf-and-pullx-files-during-checkpointed-restart/4707/3 "2022-08-31T14:33:35Z")

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Thanks, that seems to work!

By the way, it is still appending to all the files (including the pull code .xvg files)