Welcome to the TIES MD documentation.
=====================================

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   :maxdepth: 2
   :caption: Contents:

``TIES`` is a collection of software packages to calculate protein ligand binding free energies with physics based
alchemical methods. ``TIES`` stands for thermodynamic integration with enhanced sampling and can be used to calculate
accurate and reproducible relative binding free energies. Please see the theory section for more information on the
specifics of this method.

Within the ``TIES`` collection there are two packages: ``TIES 20``, ``TIES MD``. ``TIES 20`` is available online and
can be used to build all input for ``TIES MD``. ``TIES MD`` is an open source implementation of the ``TIES`` protocol that
is built on ``OpenMM`` and ``NAMD``. This document will explain the use of ``TIES MD`` software packages
please see the `TIES 20 <https://ccs-ties.org>`_ website for information on our online system builder.

Contents
=========

.. toctree::
    :maxdepth: 2

    install
    tutorial
    API
    binding_free_energies
    parallelization
    HPC_submissions
    theory
    🚀Github <https://github.com/UCL-CCS/TIES_MD>

Code Documentation
===================

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  :maxdepth: 2

  modules