iphasimulator.data.amber_openmm.run_openmm_md

Staged OpenMM MD for an Amber system (system.prmtop / system.inpcrd).

Written by iPHASimulator (notebook 06C). The stages and file names mirror the GROMACS run folders: step6.0_minimization, step6.1_nvt, step6.2_npt and step7_production. All settings come from protocol.json next to this script.

python run_openmm_md.py step6.0_minimization # local python run_openmm_md.py step6.1_nvt step6.2_npt step7_production # HPC python run_openmm_md.py –short-test # quick check

Each stage starts from the previous stage’s state (<stage>.xml) and writes <stage>.xml, <stage>.pdb and <stage>.csv; NVT/NPT/production also write <stage>.dcd frames. Every MD stage resumes from its own <stage>.chk and validates its input fingerprint from <stage>.restart.json. Completed stages take no new steps. Keep system.prmtop, system.inpcrd, this file and protocol.json together; OpenMM is required, but an iPHASimulator installation is not.

Attributes

`STAGES`
`PREVIOUS_STAGE`
`PROTEIN_RESIDUES`
`BACKBONE_ATOMS`
`SHORT_TEST_PS`
`SHORT_TEST_MINIMIZATION_ITERATIONS`

Functions

`load_protocol`(→ dict)
`stage_steps`(→ int)	Number of MD steps for a stage (0 for minimisation).
`stage_intervals`(→ tuple[float, float])	CSV and trajectory intervals in ps, with defaults for older protocol files.
`input_signature`(→ str)	Bind a restart to its topology, original coordinates and physical settings.
`validate_inputs`(→ dict)	Check particle counts, finite coordinates and a PME-compatible periodic box.
`restraint_groups`(→ tuple[list[int], list[int]])	Split heavy atoms into backbone-type and side-chain restraint groups.
`run_stage`(→ dict)	Run one stage and return a summary (energy in kJ/mol, density in g/mL).
`run_short_test`(→ list[dict])	Minimise, then 10 ps NVT and 10 ps NPT, into short_test/ (protocol settings otherwise).
`main`(→ None)

Module Contents

iphasimulator.data.amber_openmm.run_openmm_md.STAGES = ('step6.0_minimization', 'step6.1_nvt', 'step6.2_npt', 'step7_production')

iphasimulator.data.amber_openmm.run_openmm_md.PREVIOUS_STAGE

iphasimulator.data.amber_openmm.run_openmm_md.PROTEIN_RESIDUES

iphasimulator.data.amber_openmm.run_openmm_md.BACKBONE_ATOMS

iphasimulator.data.amber_openmm.run_openmm_md.SHORT_TEST_PS = 10.0

iphasimulator.data.amber_openmm.run_openmm_md.SHORT_TEST_MINIMIZATION_ITERATIONS = 1000

iphasimulator.data.amber_openmm.run_openmm_md.load_protocol(folder: str | pathlib.Path = '.') → dict

iphasimulator.data.amber_openmm.run_openmm_md.stage_steps(protocol: dict, stage: str, picoseconds: float | None = None) → int: Number of MD steps for a stage (0 for minimisation).

iphasimulator.data.amber_openmm.run_openmm_md.stage_intervals(protocol: dict, stage: str) → tuple[float, float]: CSV and trajectory intervals in ps, with defaults for older protocol files.

iphasimulator.data.amber_openmm.run_openmm_md.input_signature(folder: pathlib.Path, protocol: dict) → str: Bind a restart to its topology, original coordinates and physical settings.

iphasimulator.data.amber_openmm.run_openmm_md.validate_inputs(prmtop, inpcrd, cutoff_nm: float) → dict: Check particle counts, finite coordinates and a PME-compatible periodic box.

iphasimulator.data.amber_openmm.run_openmm_md.restraint_groups(atoms, polymer_residues) → tuple[list[int], list[int]]

Split heavy atoms into backbone-type and side-chain restraint groups.

atoms yields (index, residue_name, atom_name, element_symbol). As in the CHARMM-GUI packages: protein N/CA/C/O and polymer heavy atoms use the backbone force constant, other protein heavy atoms the side-chain one; water, ions and hydrogens are never restrained.

iphasimulator.data.amber_openmm.run_openmm_md.run_stage(stage: str, folder: str | pathlib.Path = '.', *, output_dir: str | pathlib.Path | None = None, picoseconds: float | None = None, max_iterations: int | None = None, platform_name: str | None = None) → dict: Run one stage and return a summary (energy in kJ/mol, density in g/mL).

iphasimulator.data.amber_openmm.run_openmm_md.run_short_test(folder: str | pathlib.Path = '.', *, platform_name: str | None = None) → list[dict]: Minimise, then 10 ps NVT and 10 ps NPT, into short_test/ (protocol settings otherwise).

iphasimulator.data.amber_openmm.run_openmm_md.main(argv=None) → None