Grompp checkpoint error
I’m experiencing some discrepancies when I pass the checkpoint file to
grompp using the -t checkpoint flag:
grompp -f md.mdp -o md.tpr -p topol.top -c md_res_1000.gro -t md_res_1000.cpt
This command results in a tpr file without any variables for barostat and
thermostat. These values are, however, present in the cpt file.
Running the tpr file and additionally providing the checkpoint through the
‘mdrun -cpi’ command produces a different output than running mdrun using
the same tpr (even though the checkpoint has already been passed into
#2 Updated by Mark Abraham over 2 years ago
Thanks for the report. I've amended the docs to make clear how the subsequent restart should be run.
In principle this could be made to work - old-style
gmx grompp -t traj.trr -e ener.edr still seems to have code, so code could be written to get the information from
gmx grompp -t state.cpt. However, the future of ensemble-preserving restarts will be all about the checkpoint file, and we need to reduce the number of code paths we maintain, so I will probably plan to remove some/all of
gmx grompp -t -e (in master branch sometime).