.. DROPPS documentation master file
.. ================================================================
..  index.rst — main landing page for the DROPPS documentation website
..  This file follows a structure similar to www.gromacs.org
.. ================================================================

DROPPS
=================================
**Distributed Rapid Operation Platform for Phase-separation Simulations**

**Developer**: 
- Dr. Yiming Tang, Fudan University
- Prof. Guanghong Wei, Fudan University

**DROPPS** is a high-performance molecular dynamics package designed for
simulating liquid-liquid phase separation of biomolecules such as proteins
and nucleic acids. It is implemented using OpenMM, one of the fastest MD engines
available and supports CPUs, GPUs, MPI, OpenMP, and a wide range of workflows.

This documentation hub provides comprehensive information for users,
developers, and contributors.

.. note::
   The DROPPS program is still under development. The code and manuals will be
   updated on a daily basis.

   This is a Sphinx-generated documentation site. Use the left sidebar or the
   sections below to navigate through major content areas.


Getting Started
===============

If you are new to DROPPS, the following pages help you begin:

- :doc:`quickstart/download`
- :doc:`quickstart/installation`
- :doc:`quickstart/first_simulation`
- :doc:`quickstart/faq`


User Guide
==========

The user guide describes how to set up, run, and analyze molecular dynamics
simulations with DROPPS.

.. toctree::
   :maxdepth: 2
   :caption: User Guide

   userguide/overview
   quickstart/download
   quickstart/installation
   quickstart/first_simulation
   userguide/input_files
   userguide/index_files
   userguide/simulation_workflow
   quickstart/faq


Modelling Tools
===============

The section describes how to construct a DROPPS simulation.

.. toctree::
   :maxdepth: 2
   :caption: Modelling Tools
   
   modelling/pdb2dps   
   modelling/addangle
   modelling/modifyres
   modelling/genelastic
   modelling/genmesh
   modelling/editconf
   modelling/gsd2xtc


Simulation Tools
================

The section describes how to run a DROPPS simulation.

.. toctree::
   :maxdepth: 2
   :caption: Simulation Tools
   
   simulation/grompp
   simulation/mdrun


Analysis Tools
==============

The section describes how to analysis DROPPS trajectories.

.. toctree::
   :maxdepth: 2
   :caption: Analysis Tools

   analysis/check
   analysis/extract
   analysis/trjconv
   analysis/make_ndx   
   analysis/density
   analysis/angle
   analysis/gyrate
   analysis/contact_map
   analysis/inter_distance
   analysis/intra_distance
   analysis/msd

Release Notes
=============

The following sections track major changes in recent versions.

.. toctree::
   :maxdepth: 1
   :caption: Releases

   releases/0.2.1
   releases/0.3.0

Community & Support
===================

.. toctree::
   :maxdepth: 1
   :caption: Community

   community/citations
   community/bug_reports
   community/contact

Indices and Tables
==================

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