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BP: Fachverband Biologische Physik

BP 26: Posters: Statistical Physics of Biological Systems

BP 26.5: Poster

Dienstag, 17. März 2015, 14:00–16:00, Poster A

Rigorous combination of molecular dynamics and biased or multi-temperature simulations with pytram — •Christoph Wehmeyer, Antonia Mey, Fabian Paul, Hao Wu, and Frank Noé — Institut für Mathematik, Freie Universität Berlin

The reliable estimation of equilibrium and kinetic properties of complex dynamical systems is of general interest in the physical and life sciences. Despite well established theoretical frameworks, the underlying complexity in general renders analytical predictions impossible and requires a numerical treatment instead; which can still be costly due to rare events dynamics.

Enhanced sampling and multi-ensemble methods (e.g. parallel tempering, Hamiltonian replica exchange, or umbrella sampling) allow to sample such rare events feasibly in many cases and, in this way, to calculate equilibrium properties. In general, however, the simultaneous analysis of molecular dynamics and biased simulations lacks a rigorous and broadly applicable protocol.

To this aim, we present TRAM, a fully rigorous approach to combine molecular dynamics and multi-ensemble simulations to estimate equilibrium and kinetic properties of systems with rare event dynamics using the Markov state model framework.

The TRAM method is implemented in the pytram package, available at https://github.com/markovmodel/pytram.