choderalab/yank

.. _faq:

Frequently Asked Questions (FAQ)
================================

#. Can you restart a simulation once its finished (or interrupted)?

   Yes! Either specify the :ref:`yaml_options_resume_simulation` in the YAML file, or use the
   :func:`yank.yank.AlchemicalPhase.from_storage` function to resume from existing file.

#. My setup keeps saying the system failed to create and my logfile says a bunch of things about missing "EP - OW" parameters

   The likely cause is you did choose a :ref:`solvent_model <yaml_solvents_solvent_model>` which was supported by
   the LEaP Parameters you loaded. You probably need to choose a LEaP parameter file to support your solvent model.
   E.g. the ``solvent_model`` ``tip4pew`` should have a ``leaprc.water.tip4pew`` parameter set by either a
   :ref:`molecule <yaml_molecules_leap>`, :ref:`solvent <yaml_solvents_leap>`,
   or :ref:`system wide parameter's <yaml_systems_head>` file. YANK uses the TIP4P-EW model by default.

#. Which MPI program should I use?

   We recommend the ``mpich`` and ``mpi4py`` packages that come from the ``conda-forge`` channel of ``conda``.
   These should be installed automatically if you installed YANK through conda correctly. If you use conda's MPI package,
   do *not* use your local cluster's MPI module if it has one. If you wish to use your own MPI package, make sure the
   ``mpi4py`` you install is compiled against your local MPI, otherwise you may see difficult to diagnose errors.

#. How do I add a new state to the ``protocols`` section of a YAML file?

   You can allow YANK to fully specify the alchemical protocol for you with the ``auto`` argument for the
   ``alchemical path``, instead of adding each state by hand. You can see its
   :ref:`full usage documentation <yaml_protocols_auto>` or its
   :ref:`implementation information <algorithm_auto_protocol>`

   If you want to add states by hand, follow these instructions:

   #. Find the phase you want to change in the YAML file
   #. Add an entry in each list of values for a given parameter at the index of that list where you wish to insert the state

   See the :ref:`protocols documentation <yaml_protocols_alchemical_path>` for more information or
   `watch our video guide to see how to add a state <https://youtu.be/nVVl6if6g0w?t=2m46s>`_

#. I tried to run a YAML file but it had issues setting up molecule/system/solvent that I am not using in my experiment,
   What happened?

   YANK's YAML setup process will try to build all of the molecules, systems, and solvents specified, even if they
   don't ultimately get used in a current experiment. If you don't want to process a particular object because it has
   typos, missing files, or any other issue; you can always remove the lines or comment them out with "#"

#. I found a bug or want a feature. Where do I tell you?

   Head to `YANK's GitHub page <https://github.com/choderalab/yank>`_ and post an issue.

#. I want to contribute to YANK. What is the procedure for doing so?

   #. :ref:`Install YANK from source <install_from_source>` or make a fork.
   #. Make your changes on a new branch
   #. Open a `Pull Request on GitHub <https://github.com/choderalab/yank/pulls>`_
   #. We'll discuss in on GitHub now as though it were an issue, request changes, and get your changes in!

#. What is the airspeed velocity of an unladen swallow?

   `African or European? <http://style.org/unladenswallow/>`_