Gmx mdrun -cpi -nstep option report expected files not found

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1

GROMACS version: 2023.5
GROMACS modification: No
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Hello guys, I tried to extend the running time of umbrella sampling from previous runs by using the -cpi -nstep option of mdrun, some weird results showed up

Program:     gmx mdrun, version 2023.5
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 195)
Function:    void gmx::{anonymous}::throwBecauseOfMissingOutputFiles(const std::filesystem::__cxx11::path&, gmx::ArrayRef<const gmx_file_position_t>, int, const t_filenm*, size_t)

Inconsistency in user input:
Some output files listed in the checkpoint file umbrella105.cpt are not
present or not named as the output files by the current program:)
Expected output files that are present:
  umbrella105.log
  umbrella105.xtc
  umbrella105.edr

Expected output files that are not present or named differently:
  umbrella105_pullx.xvg
  umbrella105_pullf.xvg

  It appears that pull output files were not found. It is known that using gmx
  mdrun -deffnm test with pulling and later gmx mdrun -deffnm test -cpi will
  fail to consider the changed default filename when checking the pull output
  files for restarting with appending. You may be able to work around this by
  using a command like gmx mdrun -deffnm test -px test_pullx -pf test_pullf
  -cpi.

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 explicit naming), 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. In the last
case, you will not be able to use appending in future for this simulation.

For more information and tips for troubleshooting, please check the GROMACS
website at https://manual.gromacs.org/current/user-guide/run-time-errors.html

It said that file “umbrella105_pullx.xvg and umbrella105_pullf.xvg are not present”, but it did exist:

ls umbrella105*
umbrella105.cpt  umbrella105.edr  umbrella105.gro  umbrella105.log  umbrella105_pullf.xvg  umbrella105_pullx.xvg  umbrella105.tpr  umbrella105.xtc

Still, I was able to overcome this problem using the method suggested in the error message by using the following command:
gmx mdrun -deffnm umbrella105 -px umbrella105_pullx -pf umbrella105_pullf -cpi -nsteps 50000 -update gpu -pme gpu -nb gpu

Does anyone know what the error message mean??

2

Dear @Johnla,

In my experience the error is not important in this case. Usually, the -deffnm flag is sufficient to automatically find and append the other files and continue the simulation, e.g., -deffnm prod -cpi prod.cpt will find the prod files in your directory and append to them while continuing from the state prod.cpt. However, when the pull module is active (that is, when you write the pullx and pullf files), this is not true anymore and you have to specify them, which is what you correctly did with the -px and -pf flags.