mmml run-pycharmm¶
Pure CHARMM heating/equilibration.
legacy
Legacy command. Prefer mmml md-system --backend pycharmm (no ML checkpoint). Pure MM CHARMM without MLpot; md-system covers ML workflows.
Usage¶
mmml run-pycharmm --help
Options¶
usage: mmml run-pycharmm [-h] --pdbfile PDBFILE [--cell CELL]
[--skip-setup-energy-show]
[--pycharmm-minimize/--no-pycharmm-minimize | --no-pycharmm-minimize/--no-pycharmm-minimize]
[--pycharmm-minimize-steps N]
[--two-residue-sampling | --no-two-residue-sampling]
[--two-residue-restraint-force K]
[--two-residue-restraint-r0 ANGSTROM]
[--two-residue-sampling-steps N]
[--two-residue-restraint-resid1 TWO_RESIDUE_RESTRAINT_RESID1]
[--two-residue-restraint-resid2 TWO_RESIDUE_RESTRAINT_RESID2]
[--view-braille]
Pure PyCHARMM: heating and equilibration only (no MM/ML)
Input & configuration:
--pdbfile PDBFILE Path to the PDB file (requires correct atom names and
types for CHARMM).
--two-residue-sampling, --no-two-residue-sampling
Run restrained two-residue PyCHARMM sampling after
nbonds/block setup (default: True).
--two-residue-restraint-force K
CHARMM harmonic restraint force constant for two-residue
sampling (default: 1.0).
--two-residue-restraint-r0 ANGSTROM
CHARMM harmonic restraint target distance r0 for two-
residue sampling (default: 2.5 Angstrom).
--two-residue-sampling-steps N
ABNR steps for restrained two-residue sampling (default:
--pycharmm-minimize-steps).
--two-residue-restraint-resid1 TWO_RESIDUE_RESTRAINT_RESID1
First CHARMM residue id for two-residue sampling
(default: 1).
--two-residue-restraint-resid2 TWO_RESIDUE_RESTRAINT_RESID2
Second CHARMM residue id for two-residue sampling
(default: 2).
Execution:
--skip-setup-energy-show
Skip energy.show() in setup_box for faster startup.
--pycharmm-minimize-steps N
ABNR minimization steps (default: 1000).
Diagnostics & safety:
-h, --help show this help message and exit
Other options:
--cell CELL Cubic cell side length in Å for periodic boundary
conditions (default: 1000).
--pycharmm-minimize/--no-pycharmm-minimize, --no-pycharmm-minimize/--no-pycharmm-minimize
Run PyCHARMM nbonds/minimize before heat (default:
True).
--view-braille Display braille molecular viewer at each phase.
Pure PyCHARMM runner: heating and equilibration only (no MM/ML). Runs CHARMM
setup, minimization, heating, and equilibration. Does not run ASE MD, JAX-MD, or
any ML calculator. Use this for classical CHARMM-only simulations or to prepare
structures before running mmml run (MM/ML). Usage: python -m
mmml.cli.run.run_pycharmm --pdbfile pdb/init-packmol.pdb --cell 40 mmml run-
pycharmm --pdbfile pdb/init-packmol.pdb --cell 40