AllosMod documentation
======================

AllosMod is a protocol to set up and run simulations based on a modeled
energy landscape that you create. Carefully designed energy landscapes allow
efficient molecular dynamics sampling at constant temperatures, thereby
providing ergodic sampling of conformational space. Use AllosMod to:

* Model energy landscapes for protein, DNA, RNA, and/or sugar with either
  known or modeled structures

* Sample your energy landscapes to predict often and/or rarely populated
  conformations

* Model energy landscapes for ligand-induced structural and/or dynamic
  changes, i.e. allostery

* Model energy landscapes for glycosylated proteins

Contents:

.. toctree::
   :maxdepth: 2

   installation
   usage
   glyco


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`