iphasimulator.data.amber_openmm.run_openmm_md
=============================================

.. py:module:: iphasimulator.data.amber_openmm.run_openmm_md

.. autoapi-nested-parse::

   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
----------

.. autoapisummary::

   iphasimulator.data.amber_openmm.run_openmm_md.STAGES
   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
   iphasimulator.data.amber_openmm.run_openmm_md.SHORT_TEST_MINIMIZATION_ITERATIONS


Functions
---------

.. autoapisummary::

   iphasimulator.data.amber_openmm.run_openmm_md.load_protocol
   iphasimulator.data.amber_openmm.run_openmm_md.stage_steps
   iphasimulator.data.amber_openmm.run_openmm_md.stage_intervals
   iphasimulator.data.amber_openmm.run_openmm_md.input_signature
   iphasimulator.data.amber_openmm.run_openmm_md.validate_inputs
   iphasimulator.data.amber_openmm.run_openmm_md.restraint_groups
   iphasimulator.data.amber_openmm.run_openmm_md.run_stage
   iphasimulator.data.amber_openmm.run_openmm_md.run_short_test
   iphasimulator.data.amber_openmm.run_openmm_md.main


Module Contents
---------------

.. py:data:: STAGES
   :value: ('step6.0_minimization', 'step6.1_nvt', 'step6.2_npt', 'step7_production')


.. py:data:: PREVIOUS_STAGE

.. py:data:: PROTEIN_RESIDUES

.. py:data:: BACKBONE_ATOMS

.. py:data:: SHORT_TEST_PS
   :value: 10.0


.. py:data:: SHORT_TEST_MINIMIZATION_ITERATIONS
   :value: 1000


.. py:function:: load_protocol(folder: str | pathlib.Path = '.') -> dict

.. py:function:: stage_steps(protocol: dict, stage: str, picoseconds: float | None = None) -> int

   Number of MD steps for a stage (0 for minimisation).


.. py:function:: stage_intervals(protocol: dict, stage: str) -> tuple[float, float]

   CSV and trajectory intervals in ps, with defaults for older protocol files.


.. py:function:: input_signature(folder: pathlib.Path, protocol: dict) -> str

   Bind a restart to its topology, original coordinates and physical settings.


.. py:function:: validate_inputs(prmtop, inpcrd, cutoff_nm: float) -> dict

   Check particle counts, finite coordinates and a PME-compatible periodic box.


.. py:function:: 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.


.. py:function:: 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).


.. py:function:: 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).


.. py:function:: main(argv=None) -> None