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B3: Coarse-graining of solvent effects in force-probe molecular dynamics simulations

The goal of this project is to develop multiscale schemes for efficient force probe molecular dynamics (FPMD) simulations. In all-atom (AA) simulations, pulling velocities are typically 6-8 orders of magnitude larger than in experiments. We develop hybrid schemes with an AA description for the solute and a coarse-grained (CG) procedure for the solvent to speed up FPMD simulations. In the first funding period, we have considered aprotic solvents and used Markov-state models for further dynamical coarse-graining. In the future, we plan to develop methods that allow to study also protic solvents and apply them to study molecular complexes that unfold via stable intermediates, such as calix[4]arene catenane dimer and foldamers.


Force probe simulations using a hybrid scheme with virtual sites
Ken Schäfer, Marco Oestereich, Jürgen Gauss, Gregor Diezemann
The Journal of Chemical Physics 147 (13), 134909 (2017);
doi:10.1063/1.4986194

Force probe simulations of a reversibly rebinding system: Impact of pulling device stiffness
Stefan Jaschonek, Gregor Diezemann
The Journal of Chemical Physics 146 (12), 124901 (2017);
doi:10.1063/1.4978678

Determining Factors for the Unfolding Pathway of Peptides, Peptoids, and Peptidic Foldamers
Lalita Uribe, Jürgen Gauss, Gregor Diezemann
The Journal of Physical Chemistry B 120 (40), 10433-10441 (2016);
doi:10.1021/acs.jpcb.6b06784

Mechanical unfolding pathway of a model β-peptide foldamer
Lalita Uribe, Stefan Jaschonek, Jürgen Gauss, Gregor Diezemann
The Journal of Chemical Physics 142 (20), 204901 (2015);
doi:10.1063/1.4921371

Comparative Study of the Mechanical Unfolding Pathways of α- and β-Peptides
Lalita Uribe, Jürgen Gauss, Gregor Diezemann
The Journal of Physical Chemistry B 119 (26), 8313-8320 (2015);
doi:10.1021/acs.jpcb.5b04044

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