.. autosolvate documentation master file, created by
   sphinx-quickstart on Thu Mar 15 13:55:56 2018.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to AutoSolvate's documentation!
=====================================================================
*Automated workflow to solvate molecules and run QM/MM trajectories*

.. image:: ../autosolvate/GUI/images/logo.png
   :align: center

Description
---------------------

This `open-source package <https://github.com/Liu-group/AutoSolvate/>`_ enables automated initial structure generation for explicitly solvated systems. This includes input file preparation. Additionally automated QM/MM trajectory generation and microsolvated cluster extraction is supported for the explicitly solvated systems. These features empower the user to rapidly generate large computational data sets.

AutoSolvate can be run in three ways:

#. graphical user interface (GUI)
#. command line interface (CLI)
#. Python API

Quickstart
----------------------
#. To start using AutoSolvate, you may read the :doc:`installation` page.
#. To learn to use the command line interface (CLI), you may read the :doc:`tutorial`.
#. To learn to use the graphical user interface (GUI), you may read the :doc:`tutorialGUI`.
#. To build a mixed solvent system, you may read the :doc:`tutorialMulticomponent`.
#. To generate the forcefield for metal complexes, you may read the :doc:`tutorial_for_metalcomplexes`.
#. To import AutoSolvate as a Python API, you may refer to the :doc:`api`.
 

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   installation
   tutorial
   tutorialGUI
   advancedTutorial
   tutorialMulticomponent
   tutorial_for_metalcomplexes
   mcp_setup
   api
   citation