polymerist.mdtools.openmmtools.preparation
==========================================

.. py:module:: polymerist.mdtools.openmmtools.preparation

.. autoapi-nested-parse::

   Boilerplate for setting up OpenMM Simulations and related files



Attributes
----------

.. autoapisummary::

   polymerist.mdtools.openmmtools.preparation.LOGGER


Functions
---------

.. autoapisummary::

   polymerist.mdtools.openmmtools.preparation.simulation_from_thermo
   polymerist.mdtools.openmmtools.preparation.initialize_simulation_and_files


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

.. py:data:: LOGGER

.. py:function:: simulation_from_thermo(topology: openmm.app.Topology, system: openmm.System, thermo_params: polymerist.mdtools.openmmtools.thermo.ThermoParameters, time_step: openmm.unit.Quantity, positions: Optional[openmm.unit.Quantity] = None, state: Optional[polymerist.mdtools.openmmtools.serialization.state.StateLike] = None) -> openmm.app.Simulation

   Prepare an OpenMM simulation from a serialized thermodynamics parameter set


.. py:function:: initialize_simulation_and_files(out_dir: pathlib.Path, prefix: str, sim_params: polymerist.mdtools.openmmtools.parameters.SimulationParameters, topology: openmm.app.Topology, system: openmm.System, positions: Optional[openmm.unit.Quantity] = None, state: Optional[polymerist.mdtools.openmmtools.serialization.state.StateLike] = None) -> tuple[openmm.app.Simulation, polymerist.mdtools.openmmtools.serialization.paths.SimulationPaths]

   Create simulation, bind Reporters, and update simulation Paths with newly-generated files