Usage: mlmm freq [OPTIONS]
ML/MM vibrational frequency analysis (PHVA-compatible).
Options:
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Enzyme complex PDB used by both geom_loader
and the ML/MM calculator. [required]
--parm FILE Amber parm7 topology for the full enzyme
complex. [required]
--model-pdb FILE PDB defining atoms belonging to 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.
--model-indices-one-based / --model-indices-zero-based
Interpret --model-indices as 1-based (default)
or 0-based. [default: model-indices-one-
based]
--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]
-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) 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.
--hessian-calc-mode [analytical|finitedifference]
How the ML backend builds the Hessian
(Analytical or FiniteDifference); overrides
calc.hessian_calc_mode from YAML. Default:
'FiniteDifference'. Use 'Analytical' when VRAM
is sufficient.
--max-write INTEGER Maximum number of modes to export. [default:
10]
--amplitude-ang FLOAT Mode animation amplitude (Å). [default: 0.8]
--n-frames INTEGER Frames per vibrational mode animation.
[default: 20]
--sort [value|abs] Sort modes by signed value or absolute value.
[default: value]
--temperature FLOAT Temperature (K) for thermochemistry summary.
[default: 298.15]
--pressure FLOAT Pressure (atm) for thermochemistry summary.
[default: 1.0]
--dump / --no-dump Write 'thermoanalysis.yaml' alongside the
console summary. [default: no-dump]
-o, --out-dir TEXT Output directory. [default: ./result_freq/]
--active-dof-mode [all|ml-only|partial|unfrozen]
Active DOF selection for frequency analysis:
all (all atoms), ml-only (ML only), partial
(ML + MovableMM, default), unfrozen (all non-
frozen atoms). [default: partial]
--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 frequency analysis. [default:
no-dry-run]
--ref-pdb FILE Reference PDB topology to use when --input is
XYZ (keeps XYZ coordinates).
--convert-files / --no-convert-files
Convert XYZ/TRJ outputs into PDB companions
based on the input format. [default: convert-
files]
--hess-device [auto|cuda|cpu] Device for Hessian assembly and
diagonalization (auto/cuda/cpu). Use 'cpu' to
avoid VRAM issues with large unfrozen systems.
ML model inference always uses ml_device
(typically GPU). [default: auto]
-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. [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).
--dump-hess FILE Save the computed Hessian to a compressed .npz
file. Can be loaded by 'mlmm irc --read-hess'
to avoid recomputation.
--out-json / --no-out-json Write machine-readable result.json to out_dir.
[default: no-out-json]
-h, --help Show this message and exit.