Monthly Archives: January 2015

PyTRAM – a free energy python package

Just before the weekend a colleague and I finally managed to add a new release alpha of the pytram package.
It is now on version 0.1.5 and can either be found on github:
https://github.com/markovmodel/pytram
Or the python package index:
https://pypi.python.org/pypi/pytram/0.1.5

New features are an additional free energy estimator. The package now contains dTRAM and xTRAM [1,2]. But probably the best enhancement to the previous release is the existence of a short documentation for this version. It gives a brief overview over supported input file structure, how to use the API etc. Also there are two ipython notebooks available that illustrate very basic usage examples of both estimators.

More features will follow soon.

[1] Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states H. Wu, A.S.J.S. Mey, E. Rosta, Frank Noé, J. Chem. Phys., 141 214106 (2014).

[2] xTRAM: Estimating equilibrium expectations from time-correlated simulation data at multiple thermodynamic states,  A.S.J.S. Mey,   H. Wu, and F. Noé, Phys. Rev. X, 4 041018 (2014)