The OpenMM Cookbook
===================

Getting Started
---------------

.. nbgallery::
    notebooks/cookbook/first_simulation.ipynb

Simulation Protocols
--------------------

.. nbgallery::
    notebooks/cookbook/Changing Temperature and Pressure
    notebooks/cookbook/Saving Systems to XML Files
    notebooks/cookbook/Merging Molecules
    notebooks/cookbook/Adding Hydrogens to Nonstandard Molecules

Restraints, Constraints, and External Forces
--------------------------------------------

.. nbgallery::
    notebooks/cookbook/Applying a Constant External Force
    notebooks/cookbook/Constraining Atom Positions
    notebooks/cookbook/Restraining Atom Positions
    notebooks/cookbook/Restraining Dihedrals

Analysis and System Inspection
------------------------------

.. nbgallery::
    notebooks/cookbook/Analyzing Energy Contributions
    notebooks/cookbook/Computing Interaction Energies
    notebooks/cookbook/Querying and Modifying Charges and Other Parameters
    notebooks/cookbook/report_minimization.ipynb