md
======

This option controls the molecular dynamics (MD) simulation details.

.. contents::
   :local:

.. option:: type

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      * - Value
        - ``NVE`` Microcanonical ensemble, constant number of particles, volume, and energy
      * - 
        - ``NVT`` Canonical ensemble, constant number of particles, volume, and temperature
      * - 
        - ``fep-NVE`` Free energy perturbation calculation for microcanonical ensemble
      * - 
        - ``fep-NVT`` Free energy perturbation calculation for canonical ensemble
      * - Default
        - ``NVE``
   
   Define the MD simulation type.

.. option:: dt

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      * - Value
        - A real number 
      * - Default
        - ``0.0005``

   The time step in ps. For systems not containing hydrogen atoms, ``dt`` can be set to ``0.001`` ps.

.. option:: num_steps

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      * - Value
        - An integer
      * - Default
        - ``10``
   
   The number of MD steps to be run.

.. option:: output_freq

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      * - Value
        - An integer
      * - Default
        - ``1``

   The number of steps that MD information is output. The trajectory, velocity, and gradient will be output to disk. 

.. option:: temp

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      * - Value
        - A real number
      * - Default
        - ``273.15``
   
   Define the initial temperature for NVE simulation, and the targeted temperature for NVT simulation.

.. option:: temp_nhc_length

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      * - Value
        - An integer
      * - Default
        - ``5``
   
   The length of Nose-Hoover chain to control the temperature. Usually an integer larger than 2 is enough.

.. option:: temp_nhc_tau

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      * - Value
        - A real number
      * - Default
        - ``0.5``
   
   The time-constant of Nose-Hoover chain to control the temperature in ps.

.. option:: vel_fn
   
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      * - Value
        - A file name
      * - Default
        - None

   If this is given, the initial velocities will be set from this XYZ file (in Angstrom/ps). Otherwise, velocities will be generated from Boltzmann distribution. For example:

   .. code-block:: bash
     :linenos:

     md   
       vel_fn mol-vel.xyz
     end

   Initial velocities will be read from ``mol-vel.xyz``.

.. option:: max_dr
   
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      * - Value
        - A real number
      * - Default
        - ``5``

   The maximum allowed atomic displacement per step in Angstrom. If an atom mover more than ``max_dr`` in a step, Qbics will stop the MD simulation since the system may crash due to the too fast motion.

.. option:: plumed_fn
   
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      * - Value
        - A file name
      * - Default
        - None

   If this is given, Qbics will apply enhanced sampling algorithms defined in the file in PLUMED library. For PLUMED input file grammar, please refer to its `PLUMED manual <https://www.plumed.org/doc-v2.9/user-doc/html/index.html>`_.