Mdrun cannot find pullf and pullx files during checkpointed restart

User discussions
1

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?

2

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

3

Thanks, that seems to work!

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