Extending simulations from runs on different super computers

User discussions
1

GROMACS version:2022
GROMACS modification: Yes/No
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Hi, I was running some simulations at Karolina CPU using gromacs 2022, then, I wanted to extend them locally (with the same gromacs version) and got this error (using the -noappend flag works):

Executable: /opt/tcbsys/gromacs/2022.3/gmx/AVX2_256/bin/gmx
Data prefix: /opt/tcbsys/gromacs/2022.3/gmx/AVX2_256
Working dir: /mnt/cephfs/projects/2022022600_20220226_Density_Guided_Simulations/IL23/Density_guid_Sim/Properly_alignemd_D1/No_230-271_disuphide/From_AF2_conformers/Cluster9
Command line:
gmx mdrun -v -deffnm step7_production -cpi step7_production.cpt

Program: gmx mdrun, version 2022.3
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 192)
Function: void gmx::{anonymous}::throwBecauseOfMissingOutputFiles(const char*, gmx::ArrayRef, int, const t_filenm*, size_t)

Inconsistency in user input:
Some output files listed in the checkpoint file step7_production.cpt are not
present or not named as the output files by the current program:)
Expected output files that are present:

Expected output files that are not present or named differently:

/mnt/proj2/dd-22-33/IL23/Density_guid_Sim/From_AF2_conformers/Cluster9/step7_production.log

/mnt/proj2/dd-22-33/IL23/Density_guid_Sim/From_AF2_conformers/Cluster9/step7_production.xtc

/mnt/proj2/dd-22-33/IL23/Density_guid_Sim/From_AF2_conformers/Cluster9/step7_production.edr

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.

2

I once got a similar issue in continuing a simulation where 2 of the files from the original simulation (2 .xvg files) were marked as not present despite being in the directory. Specifying those files in the actual command (adding -pf file_f.xvg -px file_x.xvg) seemed to work for me, so maybe specifying -x step7_production.xtc -g step7_production.log -e step7_production.edr would solve the issue without having to write new files (although you might want to backup your old files before trying this, I haven’t done this with files beyond .xvg files yet so I don’t know if this will still work with log, xtc and edr files or if they’ll just straight up overwrite the old files)