MD-simulation of water at constant temperature
==============================================

As an example, we will use the water molecule which you need in the xyz-format (you can download it
:download:`here <water.xyz>`). In order to set up a dynamics simulation at constant temperature, run
the GUI application with::

    metaFALCON gui

Fill in the input as in the following example.

.. figure:: nvt1.png

DFTBaby, which is chosen as a calculator, needs the molecular charge to be set explicitly. This is
done in the dialog that opens when you click the `Configure...` button.

.. figure:: nvt2.png

If you are using a different calculator, always check which options have to be set in the
`Configure...` dialog. Similarly, the Berendsen thermostat needs infomation on the temperature and
the time constant :math:`tau` for the heat bath coupling.

.. figure:: nvt3.png

We want to generate random velocities and therefore have to provide the path to the `water.xyz`
file and the sampling temperature.

After hitting `Save` from the `File` menu and closing the window, three new files have been
generated in the working directory::

    initial.xyz
    initial.vel
    meta-config.json

The first two contain the initial conditions and the latter is a json-file with the information
needed by the **metaFALCON** program to run the simulation. The ``"molecular dynamics"`` entry
within the file now reads::
   
    "molecular dynamics": {
      "do_meta": false, 
      "thermostat": {
        "tau": 100.0, 
        "type": "berendsen", 
        "temperature": 300.0
      }, 
      "initial": {
        "source": "new", 
        "xyz": "/home/user/path/to/water.xyz", 
        "temperature": 300.0
      }, 
      "interface": {
        "type": "dftbaby", 
        "configure": {
          "charge": 0
        }
      }, 
      "nsteps": 10000, 
      "tstep": 0.25
    }

To start the calculation, run::

    metaFALCON run

Afterwards, you can :doc:`analyze the results <analysis>`.