Usage: mlmm path-opt [OPTIONS]
MEP optimization via the Growing String method or Direct Max Flux.
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... Two endpoint structures (reactant/product);
both must be full-enzyme PDBs. [required]
-q, --charge INTEGER ML region 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). Defaults to 1 when
omitted.
--mep-mode [gsm|dmf] MEP optimizer: Growing String Method (gsm) or
Direct Max Flux (dmf). [default: gsm]
--dmf-backend [cpu|gpu] DMF compute backend (--mep-mode dmf only): gpu
(dmf.torch / CUDA) or cpu (dmf / NumPy). On a
GPU out-of-memory error, retry with cpu.
[default: gpu]
--max-nodes INTEGER Number of internal nodes (for GSM: string has
max_nodes+2 images including endpoints; for
DMF: number of path waypoints). [default: 20]
--max-cycles INTEGER Maximum optimization cycles. [default: 300]
--climb / --no-climb Search for a transition state (climbing image)
after path growth. [default: climb]
--preopt / --no-preopt Pre-optimize the two endpoint structures with
LBFGS before string growth. [default: preopt]
--preopt-max-cycles INTEGER Maximum LBFGS cycles for endpoint pre-
optimization when --preopt is enabled.
[default: 10000]
--fix-ends / --no-fix-ends Fix endpoint structures during path growth.
[default: fix-ends]
--dump / --no-dump Dump optimizer trajectory/restarts during the
run. [default: no-dump]
-o, --out-dir TEXT Output directory. [default:
./result_path_opt/]
--thresh [gau_loose|gau|gau_tight|gau_vtight|baker|never]
Convergence preset for the string optimizer.
--config FILE Base YAML configuration file applied before
explicit CLI options.
--show-config / --no-show-config
Print resolved configuration and continue
execution. [default: no-show-config]
--dry-run / --no-dry-run Validate options and print the execution plan
without running path optimization. [default:
no-dry-run]
--parm FILE Amber parm7 topology for the enzyme complex
(MM layers). [required]
--model-pdb FILE PDB defining the ML region (atom IDs used by
the ML/MM calculator). 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.
--freeze-atoms TEXT Comma-separated 1-based indices to freeze
(applied to every image).
--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.
--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]
--ref-pdb FILE Full-size template PDBs in the same order as
--input. Required when using XYZ inputs to
provide topology and B-factor information.
--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]
--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.