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Reweighting methods for Molecular Dynamics

Please always quote using this URN: urn:nbn:de:kobv:188-refubium-24541-6
  • The dynamical response of molecular systems, when the potential energy function is perturbed at a microscopic level, is difficult to predict without a numerical or laboratory experiment. This is due to the non-linearity and high-dimensionality of molecular systems. An efficient investigation of such a behaviour is necessary to better understand the nature of molecules and to improve the predictability of Molecular Dynamics simulations. In this thesis we propose a reweighting scheme for Markov State Models (MSMs), based on the Girsanov theorem, that permits to reduce the computational cost of the analysis when the potential energy function of a molecule is perturbed. The method has been successfully extended and implemented with metadynamics, in order to build the MSM of a molecular system in a significantly shorter computational time compared to a standard unbiased MD simulation. We also propose a new method to discretize the infinitesimal generator into a rate matrix, that could be used to efficiently study Hamiltonian perturbations as well.

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Author:Luca DonatiORCiD
Document Type:Doctoral Thesis
Publisher:Freie Universität Berlin
Granting Institution:Freie Universität Berlin
Advisor:Bettina G Keller, Marcus Weber
Date of first Publication:2019/05/08
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