mythos.simulators.gromacs
=========================

.. py:module:: mythos.simulators.gromacs

.. autoapi-nested-parse::

   GROMACS simulator module.



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/mythos/simulators/gromacs/gromacs/index
   /autoapi/mythos/simulators/gromacs/utils/index


Classes
-------

.. autoapisummary::

   mythos.simulators.gromacs.GromacsSimulator


Package Contents
----------------

.. py:class:: GromacsSimulator

   Bases: :py:obj:`mythos.simulators.base.InputDirSimulator`


   A simulator based on running a GROMACS simulation.

   This simulator runs a GROMACS simulation from an input directory containing
   the necessary configuration files and outputs a trajectory in
   `SimulatorTrajectory` format. All _file parameters refer to filenames within
   the input directory.

   :param input_dir: Path to the directory containing the GROMACS input files.
   :param energy_fn: The energy function to use for parameter updates. Parameters
                     from this energy function will be used to update the topology file.
   :param mdp_file: Name of the .mdp (molecular dynamics parameter) file.
   :param topology_file: Name of the topology file (e.g., .top). Parameters from
                         the energy function will be written to this file.
   :param trajectory_file: Name of the output trajectory file (e.g., .xtc, .trr).
   :param structure_file: Name of the structure/coordinate file (e.g., .gro, .pdb).
   :param binary_path: Path to the GROMACS binary. If not provided, will search
                       for 'gmx' in PATH.
   :param input_overrides: Key-value pairs to override in the .mdp input file.
   :param overwrite_input: Whether to overwrite the input directory or copy it.


   .. py:attribute:: energy_fn
      :type:  mythos.energy.base.EnergyFunction


   .. py:attribute:: mdp_file
      :type:  str
      :value: 'md.mdp'



   .. py:attribute:: topology_file
      :type:  str
      :value: 'topol.top'



   .. py:attribute:: structure_file
      :type:  str
      :value: 'membrane.gro'



   .. py:attribute:: index_file
      :type:  str
      :value: 'index.ndx'



   .. py:attribute:: equilibration_steps
      :type:  int
      :value: 0



   .. py:attribute:: simulation_steps
      :type:  int | None
      :value: None



   .. py:attribute:: binary_path
      :type:  pathlib.Path | None
      :value: None



   .. py:attribute:: input_overrides
      :type:  dict[str, Any]


   .. py:method:: __post_init__(*args, **kwds) -> None

      Check the validity of the configuration.



   .. py:method:: run_simulation(input_dir: pathlib.Path, opt_params: dict[str, Any] | None = None, seed: int | None = None, **_) -> mythos.simulators.base.SimulatorOutput

      Run a GROMACS simulation.

      :param input_dir: Path to the working directory for the simulation.
      :param opt_params: Optional parameters to update. These will be used to
                         update the energy function and subsequently the topology file.
      :param seed: Optional random seed for the simulation. By default, a random
                   seed is generated.

      :returns: SimulatorOutput containing the trajectory.



   .. py:method:: _run_simulation_step(structure_file: str, overrides: dict[str, Any], input_dir: pathlib.Path, step: str) -> None


   .. py:method:: _run_gromacs(cmd: list[str], cwd: pathlib.Path, log_prefix: str) -> None


   .. py:method:: _read_trajectory(input_dir: pathlib.Path) -> mythos.simulators.io.SimulatorTrajectory


   .. py:method:: _update_topology_params(input_dir: pathlib.Path, params: dict[str, Any]) -> None