Recovery

Restarting and resuming production MD

Long simulations can be interrupted. PyMACS supports checkpoint-aware restart behavior so users do not have to throw away completed work.

Files to check before resuming

  • md_0_1.cpt or another valid checkpoint file.
  • md_0_1.tpr describing the current production run.
  • md_0_1.xtc or trajectory outputs already written.
  • md_0_1.log for the last completed status.

Resume production only

Copy command 
python 2_AutomateGromacs.py --resume --production_only --ns 50

CPU-only resume

Copy command 
python 2_AutomateGromacs.py --resume --production_only --compute CPU --ns 50

Force a clean restart

Use this only when old checkpoint state is suspected to be wrong or incompatible.

Copy command 
python 2_AutomateGromacs.py --force_restart --ns 1

Important note about --ns

For restarts, --ns should describe the intended production length for the continuing production path. Always confirm logs and output timing before interpreting a resumed run.