Berlin 2015 – scientific programme

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CPP: Fachverband Chemische Physik und Polymerphysik

CPP 4: Statistical Physics in Biological Systems (joint session DY, BP, CPP)

CPP 4.5: Talk

Monday, March 16, 2015, 10:45–11:00, BH-N 243

Tackling your free energy estimates with pyfeat — •Antonia Mey, Christoph Wehmeyer, Fabian Paul, Hao Wu, and Frank Noé — Institut für Mathematik, FU Berlin

Understanding the equilibrium properties of physical systems is of general interest in many different areas of physics. In complex systems, equilibrium properties can often only be evaluated by means of numerical simulations, which are frequently plagued by rare event dynamics. One approach to circumvent rare event dynamics is to use enhanced sampling methods (e.g. replica exchange methods or umbrella sampling).

The range of established analysis methods to optimally estimate equilibrium properties from multi-ensemble simulations often requires an expert user for their implementation or even usage. Here, we introduce a new software package, the python free energy analysis toolkit -- pyfeat, that facilitates the analysis of multi-ensemble simulation. Pyfeat provides an easy-to-use interface to well established methods such as WHAM or MBAR, as well as the recently introduced transition-based reweighting analysis methods (TRAM), which borrow ideas from Markov state models. The software's straight forward usability makes comparing different estimation method applied to the same input data trivial.

Generally, any multi-ensemble simulation can be used for the analysis ranging from all-atom protein molecular dynamics simulations to simulations of condensed matter systems. Pyfeat is available for download at: https://github.com/markovmodel/pyfeat.