UmbrellaIntegrate 0.41
The umbrella integration algorithm.
License: MIT
Requires Python: >=3
Keywords: umbrella integration

UmbrellaIntegrate.py
====================

Umbrella Integration[1] algorithm of calculating PMF using Python.

Dependence
----------

-  ``Python3``
-  ``Numpy``
-  ``pandas`` for parsing metafile
-  ``Scipy`` for ``trapz`` integration

Usage:
------

See help:

.. code:: bash

    python3 ubint.py -h

Input
~~~~~

Metafile
^^^^^^^^

The ``<your-metafile>`` should be in fellowing form:

.. code:: bash

    /path/to/your/window/file window_center spring_constant [temperature]

There is a variable of ``T`` in ``ubint.py``, if the ``temperature``
left blank in the metafile, the default temperature would be variable
``T`` in the ``ubint.py``, or you can set specific temperature for some
window.

Data file for each window
^^^^^^^^^^^^^^^^^^^^^^^^^

The data file of each window need to be a 2-column file with
``time reaction_coordinate``, the coordinate should be 1-dimensional.

Output
~~~~~~

The output file is ``free_py.txt`` with 2-column
``reaction_coordinate free_energy``

Warning
-------

Unit
~~~~

I use ``kJ/mol`` in this program.

Spring constant ``K``
~~~~~~~~~~~~~~~~~~~~~

In your simulation, the biased spring potential shoud be in form of
``0.5 * K * (r - r0) ** 2``, here ``K`` is the parameter set in your
``<your-metafile>``, for some simulation program, there is no ``0.5`` in
the biased spring potential.

Screen shots
------------

Raw data was generated by `Gaussian
distribution <https://en.wikipedia.org/wiki/Normal_distribution>`__ for
each window with ``MEAN=window_center`` and ``STD=0.8``, the centers are
in range of ``0.0 ~ 19.5`` by step of ``0.5``, here is the result
compare with WHAM[2]:

-  Raw Data

.. figure:: https://raw.githubusercontent.com/Shirui816/UmbrellaIntegrate.py/master/ScreenShot/DataDetail.png
   :alt: Raw Raw
   :width: 420
   :align: center


.. figure:: https://raw.githubusercontent.com/Shirui816/UmbrellaIntegrate.py/master/ScreenShot/Data.png
   :alt: Raw IL
   :width: 420
   :align: center


-  Compare with WHAM

.. figure:: https://raw.githubusercontent.com/Shirui816/UmbrellaIntegrate.py/master/ScreenShot/PMF_UI_WHAM.png
   :alt: CMP CMP
   :width: 420
   :align: center


**The zero point in WHAM is the minimum value and the zero point in UI
is 0.**

TO DO
-----

The UI algorithm with higher oder terms[3] of ``A(xi)`` is
``ubint_ho_devel.py``, the result is not ideal using previous data,
still in development.

**Problems occurred at standard normal distributions, maybe the
quadruplicate term which even possesses a small value could cause a huge
deviation. I should try some systems with non-quadratic potentials.**

**The function ``exp(-beta(a1*xi+a2*xi^2+a3*xi^3+a4*xi^4))`` and its
integration (Normalization factor) give very large value (even inf),
this is unable to solve yet.**

Results
~~~~~~~

.. figure:: https://raw.githubusercontent.com/Shirui816/UmbrellaIntegrate.py/master/ScreenShot/ubint_ho.png
   :alt: CMP\_HO CMP\_HO
   :width: 420
   :align: center

Ref
---

1. Kästner, Johannes, and Walter Thiel. “Bridging the Gap between
   Thermodynamic Integration and Umbrella Sampling Provides a Novel
   Analysis Method: ‘Umbrella Integration.’” The Journal of Chemical
   Physics 123, no. 14 (October 8, 2005): 144104. doi:10.1063/1.2052648.
2. http://membrane.urmc.rochester.edu/content/wham
3. Kästner, Johannes. “Umbrella Integration with Higher-Order Correction
   Terms.” The Journal of Chemical Physics 136, no. 23 (June 21, 2012):
   234102. doi:10.1063/1.4729373.