The python free energy analysis toolkit has been reactivated from pyfeat https://github.com/markovmodel/pyfeat
This code is under very heavy development!
Note:
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!
TBD
- Antonia Mey <antonia.mey@ed.ac.uk>
- Antonia Mey* <antonia.mey@fu-berlin.de>
- Christoph Wehmeyer* <christoph.wehmeyer@fu-berlin.de>
- Fabian Paul
- Hao Wu
- Frank Noé
*) equal contribution
Valid for up to version 0.3.1 with Python 2.7 dependency
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 pyfeatdTRAM: 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).
Download: <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).
Download: <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)
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