GUI application
===============

The :mod:`metafalcon` package comes with a GUI application that makes it easy to set up the input for
a molecular dynamics or metadynamics run::

    metaFALCON gui

Basic input
-----------

After the start of the application, the first window you see is the molecular dynamics
configuration screen.

.. figure:: gui_md.png

At the beginning, all forms will be empty, but if there is already a 
`meta-config.json` file available in the working directory, all forms are filled automatically with 
the respective information. You can import configuration from another calculation, reset all forms
and save a `meta-config.json` file from the `File` menu.

.. hint::
    Hover over the form elements to display a descriptive tooltip help, if you are not sure what to 
    fill in.

Setting up the calculator interface
-----------------------------------

In order to provide energies and gradients for the MD run, you need to set up an interface to an
external quantum chemical calculator. Choose the desired calculator from the dropdown menu and 
click `Configure` to check if there are any options to set.

.. seealso::
    A complete list of calculator interfaces together with detailed setup instructions is given in
    :doc:`../interfaces/interfaces`.

Seting up a thermostat
----------------------

:mod:`metafalcon` allows MD simulations at constant energy or at constant temperature. For the
latter, a thermostat has to be defined that regulates the temperature in each dynamics step.

From the dropdown menu, you can choose between Berendsen and Bussi thermostats. The first is a very
common and simple thermostat that just rescales the velocities in every dynamics step dependent on
their deviation from the desired temperature. The Bussi thermostat allows for real canonical
sampling through velocity rescaling by additionally introducing a random factor. As a consequence,
a trajectory can be reproduced exactly when using the Berendsen thermostat but not when using the
Bussi thermostat.

By clicking the `Configure` button, a dialog is opened that allows to set the temperature and the
heat bath coupling constant :math:`\tau`.

.. seealso::
    An illustrative example for a MD simulation at constant temperature is given in :doc:`nvt`.

Generation of initial conditions
--------------------------------

A set of initial conditions is needed for every molecular dynamics run. These are stored in the
files `initial.xyz` (coordinates) and `initial.vel` (velocities). If a coordinates file is given,
velocities can be sampled randomly from a Maxwell-Boltzmann distribution according to a given
temperature. It is also possible to take over a set of coordinates and velocities from a previous
dynamics run. In that case, only the directory that contains the respective results is needed.

Metadynamics parameters
-----------------------

Similar to the parameters for a moleular dynamics simulation, the setup of a metadynamics run is
self-explanatory with the GUI application.

.. seealso::
    For an example of a simple metadynamics simulation, see :doc:`simplemeta`. The multistate
    metadynamics scheme is illustrated in :doc:`multistate`.