Most useful beginner flags
| Goal |
Command |
| Run a short test |
python 2_AutomateGromacs.py --ns 0.25 |
| Use CPU only |
python 2_AutomateGromacs.py --compute CPU --ns 0.25 |
| Use automatic GPU selection |
python 2_AutomateGromacs.py --compute auto --ns 0.25 |
| Use a compact box |
python 1_AutomateGromacs.py --box-type dodecahedron |
| Increase box padding |
python 1_AutomateGromacs.py --box-distance 1.2 |
| Resume an interrupted run |
python 2_AutomateGromacs.py --resume --production_only --ns 50 |
| Make contact analysis stricter |
python 3A_AutomateGromacs.py --contact_cutoff 3.5 |
| Make pocket analysis broader |
python 3A_AutomateGromacs.py --pocket-cutoff 6.0 |
Flag categories
| Category |
Examples |
| Structure input |
--pdb, --fetch-pdb, --fetch-format |
| Chain handling |
--keep-chains, --drop-chains, --chain-names, --chain-map |
| System identity |
--mode, --ligand, --cofactors |
| Box and solvent |
--box-type, --box-distance |
| MDP customization |
--mdp-dir, --em-mdp, --nvt-mdp, --npt-mdp, --md-mdp |
| Hardware |
--compute, --gpu-id, --ntomp, --ntmpi, --gmx-bin |
| Restarts |
--resume, --production_only, --force_restart |
| Analysis |
--contact_cutoff, --pocket-cutoff, --min_contact_frac |
| PROTAC |
--quick-test, --basic-only, --contacts-only, --distance-cutoff |
Beginner safety rule
Change one thing at a time. If you change the input structure, force field, box size, hardware mode, run length, and analysis cutoffs all at once, debugging becomes much harder.