Regensburg 2019 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 12: Poster II

BP 12.60: Poster

Dienstag, 2. April 2019, 14:00–16:00, Poster B2

Principal component analysis of constrained molecular dynamics simulations — •Matthias Post, Steffen Wolf, and Gerhard Stock — Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, Freiburg, Germany

Describing the structure and dynamics of biomolecular systems via conventional unbiased molecular dynamics simulations becomes impractical, if their states are separated by high energy barriers such that conformational changes of interest to not occur in reasonable computer time. One way to overcome this problem is to pull these systems with a constant force ensuring this conformational change. While data from constrained molecular dynamics simulations do not allow for a direct estimate of the free energy from their biased probability distribution, they can be readily reweighed via Jarzynski's identity to do so. Using this approach, we apply principal component analysis on these non-equilibrium data to construct a multi-dimensional free energy landscape able to distinguish between different reaction pathways. We compare unbiased and constrained data on deca-alanine, a well-established model problem of testing biased simulations and understanding fundamental mechanisms of protein folding.