Usage: mlmm scan2d [OPTIONS]
2D distance scan with harmonic restraints using the ML/MM calculator.
Options:
-v, --verbose LEVEL Console verbosity 0-3 (default 2). 0=silent;
1=milestones only; 2=+optimizer cycle tables,
per-stage timing, VRAM, deliverable paths;
3=everything (full config blocks, per-file
paths, DEBUG logging). [0<=x<=3]
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Input enzyme complex PDB (required).
[required]
--parm FILE Amber parm7 topology for the enzyme
(required). [required]
--model-pdb FILE PDB defining the ML region. Optional when
--detect-layer is enabled.
--model-indices TEXT Comma-separated atom indices for the ML region
(ranges allowed like 1-5). Used when --model-
pdb is omitted.
-q, --charge INTEGER ML-region total charge. Required unless
--ligand-charge is provided.
-l, --ligand-charge TEXT Total charge or per-resname mapping (e.g.,
GPP:-3,SAM:1) used to derive charge when -q is
omitted (requires PDB input or --ref-pdb).
-m, --multiplicity INTEGER Spin multiplicity (2S+1) for the ML region.
Defaults to 1 when omitted.
--freeze-atoms TEXT Comma-separated 1-based atom indices to freeze
(e.g., "1,3,5").
--hess-cutoff FLOAT Distance cutoff (Å) from ML region for MM
atoms to include in Hessian calculation.
Applied to movable MM atoms and can be
combined with --detect-layer.
--movable-cutoff FLOAT Distance cutoff (Å) from ML region for movable
MM atoms. MM atoms beyond this are frozen.
Providing --movable-cutoff disables --detect-
layer.
-s, --scan-lists TEXT Scan targets: inline Python literal or a
YAML/JSON spec file path.
--print-parsed / --no-print-parsed
Print parsed scan targets after resolving
--scan-lists. [default: no-print-parsed]
--config FILE Base YAML configuration file applied before
explicit CLI options.
--convert-files / --no-convert-files
Convert XYZ/TRJ outputs into PDB companions
based on the input format. [default: convert-
files]
-b, --backend [uma|orb|mace|aimnet2]
ML backend for the ONIOM high-level region
(default: uma).
--embedcharge / --no-embedcharge
Enable xTB point-charge embedding correction
for MM→ML environmental effects
(experimental). [default: no-embedcharge]
--embedcharge-cutoff FLOAT Distance cutoff (Å) from ML region for MM
point charges in xTB embedding. Default: 12.0
Å. Only used when --embedcharge is enabled.
--link-atom-method [scaled|fixed]
Link-atom position mode: scaled (g-factor,
default) or fixed (legacy 1.09/1.01 Å).
--mm-backend [hessian_ff|openmm]
MM backend: hessian_ff (analytical Hessian,
default) or openmm (finite-difference Hessian,
slower).
--cmap / --no-cmap Enable CMAP (backbone cross-map) terms in
model parm7. Default: disabled (Gaussian
ONIOM-compatible).
--out-json / --no-out-json Write machine-readable result.json to out_dir.
[default: no-out-json]
--one-based / --zero-based Interpret (i,j) indices in --scan-lists as
1-based (default) or 0-based. [default: one-
based]
--max-step-size FLOAT Maximum spacing between successive distance
targets [Å]. [default: 0.2]
--bias-k FLOAT Harmonic well strength k [eV/Å^2]. Defaults to
YAML bias.k (BIAS_KW['k']=300 in defaults.py)
when omitted; explicit CLI value overrides
YAML.
--relax-max-cycles INTEGER Maximum LBFGS cycles per biased relaxation
(also used for preopt). [default: 10000]
--dump / --no-dump Write inner d2 scan TRJs per d1 slice.
[default: no-dump]
-o, --out-dir TEXT Base output directory. [default:
./result_scan2d/]
--thresh [gau_loose|gau|gau_tight|gau_vtight|baker|never]
Convergence preset. [default: baker]
--ref-pdb FILE Reference PDB topology to use when --input is
XYZ (keeps XYZ coordinates).
--preopt / --no-preopt Run an unbiased pre-optimization. [default:
no-preopt]
--baseline [min|first] Reference for relative energy (kcal/mol):
'min' or 'first' (i=0,j=0). [default: min]
--zmin FLOAT Lower bound of the color scale (kcal/mol).
--zmax FLOAT Upper bound of the color scale (kcal/mol).
--detect-layer / --no-detect-layer
Detect ML/MM layers from input PDB B-factors
(ML=0, MovableMM=10, FrozenMM=20). If
disabled, you must provide --model-pdb or
--model-indices. [default: detect-layer]
--model-indices-one-based / --model-indices-zero-based
Interpret --model-indices as 1-based (default)
or 0-based. [default: model-indices-one-
based]
--print-every INTEGER RANGE Print optimizer status every N cycles (debug
knob). [x>=1]
--precision [fp32|fp64] MLIP backend precision: fp32 (default) or
fp64. Routed to backend-specific kwargs (UMA
precision / ORB precision / MACE
default_dtype). aimnet2: fp32 no-op; fp64
rejected.
--backend-model TEXT Model variant for the selected --backend (e.g.
uma-s-1p1 / uma-m-1p1 for uma,
orb_v3_conservative_omol for orb, MACE-OMOL-0
/ MACE-OFF23_small for mace). Default: the
backend's built-in model.
--calc-file FILE Python file exposing get_calculator(...) -> an
ASE Calculator used as the ML-region backend
(overrides --backend). Couples GFN-xTB / DFTB+
/ any ASE engine. See --calc-factory.
--calc-factory TEXT Name of the callable in --calc-file that
returns an ASE Calculator (or a module-level
Calculator instance). [default:
get_calculator]
--deterministic / --no-deterministic
Strict bit-reproducible GPU runs
(deterministic algorithms + index_reduce_
shim). Slower; raises if unsupported. Default
off.
--allow-charge-mult-mismatch Skip the ML-region charge/multiplicity
electron-parity check (logs that it was
skipped). For an intentional open-shell or
covalently-cut ML region.
-h, --help Show this message and exit.