Usage: mlmm irc [OPTIONS]
Run an IRC calculation with EulerPC. Only the documented CLI options are
accepted; all other settings come from YAML.
Options:
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Input structure file (.pdb, .xyz, _trj.xyz,
etc.). [required]
--parm FILE Amber parm7 topology for the whole enzyme (MM
region). If omitted, must be provided in YAML
as calc.real_parm7.
--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
(B=0/10/20). If disabled, you must provide
--model-pdb or --model-indices. [default:
detect-layer]
-q, --charge INTEGER Total charge; overrides calc.charge from YAML.
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); overrides calc.spin
from YAML.
--max-cycles INTEGER Maximum number of IRC steps; overrides
irc.max_cycles from YAML.
--step-size FLOAT Step length in mass-weighted coordinates;
overrides irc.step_length from YAML.
--root INTEGER Imaginary mode index used for the initial
displacement; overrides irc.root from YAML.
--forward / --no-forward Run the forward IRC; overrides irc.forward
from YAML.
--backward / --no-backward Run the backward IRC; overrides irc.backward
from YAML.
-o, --out-dir TEXT Output directory; overrides irc.out_dir from
YAML. [default: ./result_irc/]
--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.
--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 IRC. [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]
-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 when --embedcharge is enabled.
-h, --help Show this message and exit.