==========================================
 Biomolecular QM/MM with CP2K and GROMACS
==========================================

This guide provides practical advice on how to use CP2K and the GROMACS-CP2K interface
to perform QM/MM simulation of biomolecular systems.

For *general methodological* advice on QM/MM modelling & simulation of biomolecular
systems, see our guide on `Best Practices in QM/MM Simulation of Biomolecular Systems <https://docs.bioexcel.eu/qmmm_simulation_bpg>`_



.. toctree::
   :maxdepth: 2
   :caption: Overview:

   overview/overview
	      
.. toctree::
   :maxdepth: 2
   :caption: System preparation:

   system_preparation/system_preparation
   system_preparation/selecting_qm_atoms

.. toctree::
   :maxdepth: 2
   :caption: Input preparation:

   input_preparation/CP2K_MM_setup
   input_preparation/QM_treatment
   input_preparation/CP2K_QMMM_parameterisation
   input_preparation/interface_QMMM_parameterisation
   
.. toctree::
   :maxdepth: 2
   :caption: Running:

   running_cp2k/building_cp2k
   running_cp2k/running_cp2k
   running_cp2k/cp2k_output
   running_cp2k/cp2k_errors