@phdthesis{Donati2019, author = {Donati, Luca}, title = {Reweighting methods for Molecular Dynamics}, publisher = {Freie Universit{\"a}t Berlin}, doi = {10.17169/refubium-2305}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:188-refubium-24541-6}, year = {2019}, abstract = {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.}, language = {en} }