Regensburg 2013 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 8: Posters: Proteins
BP 8.24: Poster
Montag, 11. März 2013, 17:30–19:30, Poster B2
Adjusting a Langevin model to Molecular Dynamics — •Norbert Schaudinnus1, Andrzej Rzepiela1, Rainer Hegger2, and Gerhard Stock1 — 1Biomolecular Dynamics, Physikalisches Institut, Universität Freiburg, Hermann-Herder-Str. 3, 79104 Freibur — 2J.W. Goethe University, Institute for Physical and Theoretical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt/Main
Molecular Dynamics simulations (MD) are nowadays routinely used to investigate the behaviour of proteins, employing huge amounts of resources to propagate the Newtonian equations of motion for each atom. The Langevin formalism provides a method to recover those dynamics, based on a reduced subset of collective coordinates. Describing the time evolution as a superposition of drift and diffusive motion, the Langevin approach has been shown to correctly reproduce the conformational dynamics of polyalanines [1]. Using local estimates to compute the corresponding fields from MD trajectories, the method contains parameters, which determine the accuracy of the Langevin approach. We investigate this dependence providing a strategy to optimize the Langevin technique. We further demonstrate a method to reduce the amount of underlying data used to compute our estimates in a reliable way to further increase the efficiency of our method. We show the application of our method for various peptide systems. [1] R. Hegger and G. Stock, J. Chem. Phys. 130, 034106 (2009)