Quickstart: mlmm all

Goal

Run the end-to-end workflow once from two full PDB structures.

Minimal command

mlmm all -i R.pdb P.pdb -c 'SAM,GPP' -l 'SAM:1,GPP:-3' --out-dir ./result_all

If you want post-processing in the same run:

mlmm all -i R.pdb P.pdb -c 'SAM,GPP' -l 'SAM:1,GPP:-3' \
 --tsopt --thermo --dft --out-dir ./result_all

What to check

  • result_all/summary.log

  • result_all/summary.yaml

  • result_all/path_search/mep.pdb (or segment outputs under result_all/path_search/seg_*/)

Tips

  • Use --dry-run (shown in --help-advanced) to validate parsing and execution plan without running heavy stages.

  • mlmm all --help shows core options; mlmm all --help-advanced shows the full list including --dry-run.

  • To use a different MLIP backend, add -b orb (or mace, aimnet2). Default is uma.

  • Add --embedcharge to enable xTB point-charge embedding for MM-to-ML environmental corrections.

Next step