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

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

.. autoapi-nested-parse::

   Utilities for the GROMACS simulator.



Attributes
----------

.. autoapisummary::

   mythos.simulators.gromacs.utils.ANGSTROMS_TO_NM
   mythos.simulators.gromacs.utils.logger


Functions
---------

.. autoapisummary::

   mythos.simulators.gromacs.utils.read_trajectory_mdanalysis
   mythos.simulators.gromacs.utils.preprocess_topology


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

.. py:data:: ANGSTROMS_TO_NM
   :value: 0.1


.. py:data:: logger

.. py:function:: read_trajectory_mdanalysis(topology_file: pathlib.Path, trajectory_file: pathlib.Path) -> mythos.simulators.io.SimulatorTrajectory

   Read a GROMACS trajectory using MDAnalysis.

   :param topology_file: Path to the topology file (e.g., output.tpr).
   :param trajectory_file: Path to the trajectory file (e.g., output.trr).

   :returns: SimulatorTrajectory containing the rigid body trajectory data.


.. py:function:: preprocess_topology(input_dir: str | pathlib.Path, params: dict | None = None, copy_to: pathlib.Path | None = None, output_prefix: str = 'preprocessed', output_mdp_name: str = 'preprocessed.mdp', gromacs_binary: str | pathlib.Path | None = None, mdp_name: str = 'md.mdp', topology_name: str = 'topol.top', structure_name: str = 'membrane.gro', index_name: str = 'index.ndx', log_prefix: str = 'topology_preprocess') -> None

   Preprocess a GROMACS topology.

   This function runs `gmx grompp` to preprocess the GROMACS topology, applying
   any parameter updates to the .mdp file as needed. The preprocessed topology
   will be saved with the specified output prefix. Optionally copies input
   files to a new location to avoid modifying originals.

   :param input_dir: Directory containing the GROMACS input files.
   :param params: Optional dictionary of parameters to update in the .mdp file.
   :param copy_to: Optional directory to copy input files to before preprocessing.
                   If the directory exists, an exception is raised.
   :param output_prefix: Prefix for the preprocessed topology (.top extension)
                         and tpr files (.tpr extension).
   :param output_mdp_name: Name of the output .mdp file after replacements.
   :param gromacs_binary: Optional path to the GROMACS binary (defaults to 'gmx' in PATH).
   :param mdp_name: Name of the .mdp file in the input directory.
   :param topology_name: Name of the topology file in the input directory.
   :param structure_name: Name of the structure file in the input directory.
   :param index_name: Name of the index file in the input directory.
   :param log_prefix: Prefix for log messages.