Metadata-Version: 1.2
Name: UmbrellaIntegrate
Version: 0.41
Summary: The umbrella integration algorithm.
Home-page: https://github.com/shirui816/UmbrellaIntegrate.py
Author: Shirui
Author-email: Shirui816@gmail.com
License: MIT
Description-Content-Type: UNKNOWN
Description: 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.
        
Keywords: umbrella integration
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: POSIX :: Linux
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3
