The python free energy analysis toolkit.
This code is under very heavy development!
Currently the following algorithms are featured:
In future releases the list of available free energy algorithms will be extended. Watch this space!
With pip from PyPI:
# you might have to install these dependencies manually pip install cython pip install numpy pip install pytram # install pyfeat pip install pyfeat
With using conda:
#Conda should automoatically take care of all dependencies conda install -c https://conda.binstar.org/omnia pytram
- Antonia Mey* <firstname.lastname@example.org>
- Christoph Wehmeyer* <email@example.com>
- Fabian Paul
- Hao Wu
- Frank Noé
*) equal contribution
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).
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).
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)
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