iphasimulator.simulation_openmm_amber_runner
============================================

.. py:module:: iphasimulator.simulation_openmm_amber_runner

.. autoapi-nested-parse::

   OpenMM runner for AMBER topology files.



Exceptions
----------

.. autoapisummary::

   iphasimulator.simulation_openmm_amber_runner.OpenMMRunnerError


Classes
-------

.. autoapisummary::

   iphasimulator.simulation_openmm_amber_runner.OpenMMOutputs
   iphasimulator.simulation_openmm_amber_runner.OpenMMStageTimings


Functions
---------

.. autoapisummary::

   iphasimulator.simulation_openmm_amber_runner.openmm_available
   iphasimulator.simulation_openmm_amber_runner.run_openmm_with_amber_topology


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

.. py:class:: OpenMMOutputs

   Files produced by an OpenMM AMBER-topology run.


   .. py:attribute:: output_dir
      :type:  pathlib.Path


   .. py:attribute:: minimized_pdb_path
      :type:  pathlib.Path


   .. py:attribute:: trajectory_path
      :type:  pathlib.Path


   .. py:attribute:: state_xml_path
      :type:  pathlib.Path


   .. py:attribute:: log_path
      :type:  pathlib.Path


   .. py:attribute:: nvt_trajectory_path
      :type:  pathlib.Path


   .. py:attribute:: nvt_log_path
      :type:  pathlib.Path


   .. py:attribute:: npt_trajectory_path
      :type:  pathlib.Path


   .. py:attribute:: npt_log_path
      :type:  pathlib.Path


   .. py:attribute:: production_trajectory_path
      :type:  pathlib.Path


   .. py:attribute:: production_log_path
      :type:  pathlib.Path


   .. py:attribute:: final_pdb_path
      :type:  pathlib.Path


   .. py:attribute:: summary_log_path
      :type:  pathlib.Path


.. py:class:: OpenMMStageTimings

   Wall-clock timings for an OpenMM AMBER workflow.


   .. py:attribute:: minimization_seconds
      :type:  float


   .. py:attribute:: nvt_seconds
      :type:  float


   .. py:attribute:: npt_seconds
      :type:  float


   .. py:attribute:: production_seconds
      :type:  float


.. py:exception:: OpenMMRunnerError



   Raised when OpenMM is unavailable or simulation setup fails.


.. py:function:: openmm_available() -> bool

   Return True when OpenMM can be imported.


.. py:function:: run_openmm_with_amber_topology(prmtop_path: str | pathlib.Path, inpcrd_path: str | pathlib.Path, output_dir: str | pathlib.Path, *, temperature_kelvin: float = 300.0, friction_per_picosecond: float = 1.0, timestep_femtoseconds: float = 2.0, minimization_max_iterations: int = 200, simulation_steps: int = 100, nvt_steps: int | None = None, npt_steps: int = 100, production_steps: int = 100, report_interval: int = 10, pressure_bar: float = 1.0, nonbonded_cutoff_nanometers: float = 1.0, platform_name: str | None = None, platform_precision: str | None = 'mixed') -> OpenMMOutputs

   Run minimization, NVT, NPT when periodic, and production from AMBER files.