.. title:: amx .. sectnum:: :depth: 3 **"Automatic GROMACS"** (a.k.a. AUTOMACS or just **amx** for short) is a biophysics simulation pipeline designed to help you run scalable, reproducible, and extensible simulations using the popular `GROMACS `_ integrator. The documentation :ref:`walkthrough ` below describes how the codes work (and how you should use them). The :ref:`components ` section describes the codes available in **this particular** copy of automacs, including any extensions you may have downloaded. Everything but the kitchen sink can be found by :ref:`searching ` the :ref:`index `. Before starting the walkthrough, you must collect additional automacs modules by running the following :any:`setup ` command with the ``all`` recipe. If this is your first time running automacs on a particular computer, you should also :ref:`configure the gromacs paths ` by running :any:`make gromacs_config `. .. code-block :: bash make gromacs_config local make setup all .. _contents: The following sections explain how you can interact with the codes and outline the relatively minimal set of design constraints required for extending the codes to new use cases. The :ref:`components ` section at the end includes the "live" documentation for your extension modules. .. include:: concept.rst .. include:: configuration.rst .. include:: interface.rst .. include:: framework.rst .. try: toctree:: :glob: :maxdepth: 1 ... and a list of the top-level rst files if you want them on separate pages .. _components: Components ========== This section catalogs the codes loaded into the current copy of automacs. It parses the codes according to the local copy of :doc:`config.py `, which configures the connections to external codes. proteins -------- The ``Proteins`` extension is a component of automacs located at ``amx/proteins`` and sourced from ``http://github.com/biophyscode/amx-proteins.git``. .. toctree:: :maxdepth: 4 amx-proteins/scripts.rst amx-proteins/experiments.rst bilayers -------- The ``Bilayers`` extension is a component of automacs located at ``inputs/bilayers`` and sourced from ``http://github.com/bradleyrp/amx-bilayers.git``. .. toctree:: :maxdepth: 4 inputs-bilayers/scripts.rst inputs-bilayers/experiments.rst inputs-bilayers/submodules.rst charmm ------ The ``Charmm`` extension is a component of automacs located at ``inputs/charmm`` and sourced from ``http://github.com/bradleyrp/amx-charmm.git``. .. toctree:: :maxdepth: 4 inputs-charmm/modules.rst docs ---- The ``Docs`` extension is a component of automacs located at ``inputs/docs`` and sourced from ``http://github.com/bradleyrp/amx-docs.git``. .. toctree:: :maxdepth: 4 inputs-docs/scripts.rst inputs-docs/modules.rst extras ------ The ``Extras`` extension is a component of automacs located at ``inputs/extras`` and sourced from ``http://github.com/bradleyrp/amx-extras.git``. .. toctree:: :maxdepth: 4 inputs-extras/scripts.rst inputs-extras/experiments.rst inputs-extras/modules.rst martini ------- The ``Martini`` extension is a component of automacs located at ``inputs/martini`` and sourced from ``http://github.com/bradleyrp/amx-martini.git``. .. toctree:: :maxdepth: 4 inputs-martini/scripts.rst inputs-martini/experiments.rst inputs-martini/modules.rst polymers -------- The ``Polymers`` extension is a component of automacs located at ``inputs/polymers`` and sourced from ``http://github.com/bradleyrp/amx-polymers.git``. .. toctree:: :maxdepth: 4 inputs-polymers/scripts.rst inputs-polymers/experiments.rst vmd --- The ``Vmd`` extension is a component of automacs located at ``inputs/vmd`` and sourced from ``http://github.com/bradleyrp/amx-vmd.git``. .. toctree:: :maxdepth: 4 inputs-vmd/experiments.rst inputs-vmd/modules.rst