py_estimate

The Python free energy analysis toolkit.

Note

This code is under very heavy development!

Currently the following algorithms are featured:

• WHAM
• DTRAM
• xTRAM

In future releases the list of available free energy algorithms will be extended. Watch this space!

Installation

The following dependencies should be satisfied:

• cython
• numpy

From py_estimate main folder, type python setup.py install

Authors

• Antonia Mey * [email protected]
• Christoph Wehmeyer * [email protected]
• Fabian Paul
• Hao Wu
• Frank Noé

* equal contribution

References

• dTRAM: Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states, Hao Wu, Antonia S.J.S. Mey, Edina Rosta, and Frank Noé, J. Chem. Phys. 141, 214106 (2014). http://scitation.aip.org/content/aip/journal/jcp/141/21/10.1063/1.4902240

• xTRAM: Estimating Equilibrium Expectations from Time-Correlated Simulation Data at Multiple Thermodynamic States, Antonia S.J.S. Mey, Hao Wu, and Frank Noé, Phys. Rev. X 4, 041018 (2014). http://journals.aps.org/prx/pdf/10.1103/PhysRevX.4.041018

• WHAM: The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method, Shankar Kumar, John M. Rosenberg, Djamal Bouzida, Robert H. Swendsen and Peter A. Kollman, J. Comput. Chem. 13, 1011–1021 (1992) http://onlinelibrary.wiley.com/doi/10.1002/jcc.540130812/abstract;jsessionid=096E6ED4241821B755F9424DCE203430.f03t02

Copyright notice

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

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