BPCPPDYSOE21 – scientific programme

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BP: Fachverband Biologische Physik

BP 24: Poster B: Active Biological Matter, Cell Mechanics, Systems Biology, Computational Biophysics, etc.

BP 24.43: Poster

Tuesday, March 23, 2021, 16:00–18:30, BPp

Protein-ligand dynamics on multisecond timescales from sub-µs atomistic simulations — •Steffen Wolf, Benjamin Lickert, Simon Bray, and Gerhard Stock — Biomolecular Dynamics, Institute of Physics, University of Freiburg, Hermann-Herder-Straße 3a, 79104 Freiburg

Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal to allow the prediction of processes occurring on biologically relevant timescales. To achieve the necessary enhanced sampling, we first perform dissipation-corrected targeted molecular dynamics simulations which yield free energy and friction profiles of the molecular process of interest. In a second step, we use these fields to perform Langevin equation simulations which account for the desired molecular kinetics. By introducing the concept of temperature boosting of the Langevin equation, this combination of methods allows for the simulation of biomolecular processes occurring on multisecond timescales and beyond. Adopting the dissociation of solvated sodium chloride and several protein-ligand complexes as test problems, we are able to reproduce rates from atomistic MD simulation and experiments within a factor of 1.5–4 for rates up to the range of millseconds and 2–20 in the range of seconds.