.. tip::
    All input files can be downloaded: :download:`Files <https://zhjun-sci.com/qbics/input_library/tutorials-emd.tar.xz>`.

.. tip::
    For more information of this section, please refer to these keywords:

    - :doc:`../keywords/md`
    - Plumed tutorial: `<https://www.plumed.org/doc-v2.9/user-doc/html/index.html>`_

Molecular Dynamics Simulations with Enhanced Sampling
=================================================================

.. contents::
   :local:

This tutorial will lead you step by step to do molecular dynamics (MD) simulations with enhanced sampling using Qbics. Assume you have read :doc:`md`, :doc:`opt`, :doc:`dft` or :doc:`charmm`. 

Although standard MD is very important, it may take too long for a system to go across high barriers to enable the occurance of chemical reactions or large amplitute motions. Such processes are called **rare events.** To enable us to sample the rare events in short time-scale, we need to add **bias potentials** on some **collective coordinates** to accelerate specific processes. This is the so-called **enhanced sampling** MD. In Qbics, such algorithms are implmented in `Plumed <https://github.com/plumed/plumed2/releases/>`_ library. As long as you have ever learned Plumed, you can use all its functions combined with DFT, semi-empirical, MM or QM/MM methods in Qbics. You just need add ``plumed_fn`` in ``md...end``, enhaned sampling will be automatically activated:

.. code-block::
    :linenos:

    md
        plumed_fn pl.dat
    end

where ``pl.dat`` is the name of the file that gives Plumed settings like:

.. code-block::
    :caption: pl.dat
    :linenos:

    d1:  DISTANCE ATOMS=319,320
    PRINT ARG=d1 STRIDE=100 FILE=COLVAR

For a complete tutorial of Plumed, please refer to: `<https://www.plumed.org/doc-v2.9/user-doc/html/index.html>`_.
    
Example: XXXXXX
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