{ "info": { "author": "Shirui", "author_email": "Shirui816@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Operating System :: POSIX :: Linux", "Programming Language :: Python :: 3", "Topic :: Scientific/Engineering :: Chemistry", "Topic :: Scientific/Engineering :: Physics" ], "description": "UmbrellaIntegrate.py\n====================\n\nUmbrella Integration[1] algorithm of calculating PMF using Python.\n\nDependence\n----------\n\n- ``Python3``\n- ``Numpy``\n- ``pandas`` for parsing metafile\n- ``Scipy`` for ``trapz`` integration\n\nUsage:\n------\n\nSee help:\n\n.. code:: bash\n\n python3 ubint.py -h\n\nInput\n~~~~~\n\nMetafile\n^^^^^^^^\n\nThe ```` should be in fellowing form:\n\n.. code:: bash\n\n /path/to/your/window/file window_center spring_constant [temperature]\n\nThere is a variable of ``T`` in ``ubint.py``, if the ``temperature``\nleft blank in the metafile, the default temperature would be variable\n``T`` in the ``ubint.py``, or you can set specific temperature for some\nwindow.\n\nData file for each window\n^^^^^^^^^^^^^^^^^^^^^^^^^\n\nThe data file of each window need to be a 2-column file with\n``time reaction_coordinate``, the coordinate should be 1-dimensional.\n\nOutput\n~~~~~~\n\nThe output file is ``free_py.txt`` with 2-column\n``reaction_coordinate free_energy``\n\nWarning\n-------\n\nUnit\n~~~~\n\nI use ``kJ/mol`` in this program.\n\nSpring constant ``K``\n~~~~~~~~~~~~~~~~~~~~~\n\nIn your simulation, the biased spring potential shoud be in form of\n``0.5 * K * (r - r0) ** 2``, here ``K`` is the parameter set in your\n````, for some simulation program, there is no ``0.5`` in\nthe biased spring potential.\n\nScreen shots\n------------\n\nRaw data was generated by `Gaussian\ndistribution `__ for\neach window with ``MEAN=window_center`` and ``STD=0.8``, the centers are\nin range of ``0.0 ~ 19.5`` by step of ``0.5``, here is the result\ncompare with WHAM[2]:\n\n- Raw Data\n\n.. figure:: https://raw.githubusercontent.com/Shirui816/UmbrellaIntegrate.py/master/ScreenShot/DataDetail.png\n :alt: Raw Raw\n :width: 420\n :align: center\n\n\n.. figure:: https://raw.githubusercontent.com/Shirui816/UmbrellaIntegrate.py/master/ScreenShot/Data.png\n :alt: Raw IL\n :width: 420\n :align: center\n\n\n- Compare with WHAM\n\n.. figure:: https://raw.githubusercontent.com/Shirui816/UmbrellaIntegrate.py/master/ScreenShot/PMF_UI_WHAM.png\n :alt: CMP CMP\n :width: 420\n :align: center\n\n\n**The zero point in WHAM is the minimum value and the zero point in UI\nis 0.**\n\nTO DO\n-----\n\nThe UI algorithm with higher oder terms[3] of ``A(xi)`` is\n``ubint_ho_devel.py``, the result is not ideal using previous data,\nstill in development.\n\n**Problems occurred at standard normal distributions, maybe the\nquadruplicate term which even possesses a small value could cause a huge\ndeviation. I should try some systems with non-quadratic potentials.**\n\n**The function ``exp(-beta(a1*xi+a2*xi^2+a3*xi^3+a4*xi^4))`` and its\nintegration (Normalization factor) give very large value (even inf),\nthis is unable to solve yet.**\n\nResults\n~~~~~~~\n\n.. figure:: https://raw.githubusercontent.com/Shirui816/UmbrellaIntegrate.py/master/ScreenShot/ubint_ho.png\n :alt: CMP\\_HO CMP\\_HO\n :width: 420\n :align: center\n\nRef\n---\n\n1. K\u00e4stner, Johannes, and Walter Thiel. \u201cBridging the Gap between\n Thermodynamic Integration and Umbrella Sampling Provides a Novel\n Analysis Method: \u2018Umbrella Integration.\u2019\u201d The Journal of Chemical\n Physics 123, no. 14 (October 8, 2005): 144104. doi:10.1063/1.2052648.\n2. http://membrane.urmc.rochester.edu/content/wham\n3. K\u00e4stner, Johannes. \u201cUmbrella Integration with Higher-Order Correction\n Terms.\u201d The Journal of Chemical Physics 136, no. 23 (June 21, 2012):\n 234102. doi:10.1063/1.4729373.\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/shirui816/UmbrellaIntegrate.py", "keywords": "umbrella integration", "license": "MIT", "maintainer": "", "maintainer_email": "", "name": "UmbrellaIntegrate", "package_url": "https://pypi.org/project/UmbrellaIntegrate/", "platform": "", "project_url": "https://pypi.org/project/UmbrellaIntegrate/", "project_urls": { "Homepage": "https://github.com/shirui816/UmbrellaIntegrate.py" }, "release_url": "https://pypi.org/project/UmbrellaIntegrate/0.41/", "requires_dist": [ "numpy", "scipy", "pandas" ], "requires_python": ">=3", "summary": "The umbrella integration algorithm.", "version": "0.41" }, "last_serial": 3735216, "releases": { "0.41": [ { "comment_text": "", "digests": { "md5": "7bca97e59ad30d2d90898750cbb191ce", "sha256": "0b074941fc276c50ed26207c71f7c0f765957bd2c7707a1ac9358ed836102558" }, "downloads": -1, "filename": "UmbrellaIntegrate-0.41-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "7bca97e59ad30d2d90898750cbb191ce", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": ">=3", "size": 7437, "upload_time": "2018-04-04T20:12:37", "url": "https://files.pythonhosted.org/packages/2d/30/4bc93340ebb951f2b6601c02fbae8eee0baea12fae4c1bd0049edbed424e/UmbrellaIntegrate-0.41-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "4c87ec03f9c9b60b9791bea7b9e2e95d", "sha256": "c068c648eab7cd7c6c0feda793b12cced51c91b17b0af52fd0292bd5fe0ecc69" }, "downloads": -1, "filename": "UmbrellaIntegrate-0.41-py3-none-any.whl", "has_sig": false, "md5_digest": "4c87ec03f9c9b60b9791bea7b9e2e95d", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3", "size": 7427, "upload_time": "2018-04-04T20:12:39", "url": "https://files.pythonhosted.org/packages/8a/5b/d03f75892b7f34dff961ef4fd47e4b9bd2f768c2d394c22483f660d7c107/UmbrellaIntegrate-0.41-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "d53c57277cc005f2841f293f12f22ce6", "sha256": "feff335412622dad0dd1a4b75fd7e1a8a8a0ec62e366467c215749f85bb2219b" }, "downloads": -1, "filename": "UmbrellaIntegrate-0.41.tar.gz", "has_sig": true, "md5_digest": "d53c57277cc005f2841f293f12f22ce6", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3", "size": 5491, "upload_time": "2018-04-04T20:12:40", "url": "https://files.pythonhosted.org/packages/05/0b/716a285345a65912f6b982ce2d5a1ae557058f05af2dbbb08caed02fed79/UmbrellaIntegrate-0.41.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "7bca97e59ad30d2d90898750cbb191ce", "sha256": "0b074941fc276c50ed26207c71f7c0f765957bd2c7707a1ac9358ed836102558" }, "downloads": -1, "filename": "UmbrellaIntegrate-0.41-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "7bca97e59ad30d2d90898750cbb191ce", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": ">=3", "size": 7437, "upload_time": "2018-04-04T20:12:37", "url": "https://files.pythonhosted.org/packages/2d/30/4bc93340ebb951f2b6601c02fbae8eee0baea12fae4c1bd0049edbed424e/UmbrellaIntegrate-0.41-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "4c87ec03f9c9b60b9791bea7b9e2e95d", "sha256": "c068c648eab7cd7c6c0feda793b12cced51c91b17b0af52fd0292bd5fe0ecc69" }, "downloads": -1, "filename": "UmbrellaIntegrate-0.41-py3-none-any.whl", "has_sig": false, "md5_digest": "4c87ec03f9c9b60b9791bea7b9e2e95d", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3", "size": 7427, "upload_time": "2018-04-04T20:12:39", "url": "https://files.pythonhosted.org/packages/8a/5b/d03f75892b7f34dff961ef4fd47e4b9bd2f768c2d394c22483f660d7c107/UmbrellaIntegrate-0.41-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "d53c57277cc005f2841f293f12f22ce6", "sha256": "feff335412622dad0dd1a4b75fd7e1a8a8a0ec62e366467c215749f85bb2219b" }, "downloads": -1, "filename": "UmbrellaIntegrate-0.41.tar.gz", "has_sig": true, "md5_digest": "d53c57277cc005f2841f293f12f22ce6", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3", "size": 5491, "upload_time": "2018-04-04T20:12:40", "url": "https://files.pythonhosted.org/packages/05/0b/716a285345a65912f6b982ce2d5a1ae557058f05af2dbbb08caed02fed79/UmbrellaIntegrate-0.41.tar.gz" } ] }