GROMACS version: 2020.2
GROMACS modification: No
Hello, I am trying to extend a simulation and have encountered a possible bug. I extended with:
gmx convert-tpr -s md01.tpr -extend 10070 -o md02.tpr
and ran with:
gmx mdrun -v -c md02.pdb -deffnm md02 -cpi md01.cpt
which outputted:
GROMACS: gmx mdrun, version 2020.2
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /mnt/c/My Documents/data/JAS_00643 - SP-ET/gromacs/fadh2-a2q
Command line: gmx mdrun -v -c md02.pdb -deffnm md02 -cpi md01.cpt
Program: gmx mdrun, version 2020.2
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 159) 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 md01.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:
md01.log
md01.xtc
md01.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 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 http://www.gromacs.org/Documentation/Errors
however ls gives:
/mnt/c/My Documents/data/JAS_00643 - SP-ET/gromacs/fadh2-a2q$ ls md01*
md01.cpt md01.edr md01.log md01.pdb md01.tpr md01.xtc md01_part.xtc md01_prev.cpt
So all the files are there and the directory structure hasn’t changed. I’m thinking it might be the inclusion of spaces in the directory names? Is there any way to explicitly input the files to mdrun so I can append? Or is it too late for this simulation now?
Many thanks,
Steve