@inproceedings{FackeldeyBujotzek, author = {Fackeldey, Konstantin and Bujotzek, Alexander}, title = {Local Quantum-Like Updates in Classical Molecular Simulation Realized Within an Uncoupling-Coupling Approach}, series = {Progress in Industrial Mathematics at ECMI 2012}, volume = {19}, booktitle = {Progress in Industrial Mathematics at ECMI 2012}, doi = {10.1007/978-3-319-05365-3_42}, pages = {309 -- 313}, abstract = {In this article a method to improve the precision of the classical molecular dynamics force field by solving an approximation problem with scattered quantum mechanical data is presented. This novel technique is based on two steps. In the first step a partition of unity scheme is used for partitioning the state space by meshfree basis functions. As a consequence the potential can be localized for each basis function. In a second step, for one state in each meshfree basis function, the precise QM-based charges are computed. These local QM-based charges are then used, to optimize the local potential function. The performance of this method is shown for the alanine tripeptide.}, language = {en} } @inproceedings{FackeldeyBujotzekWeber, author = {Fackeldey, Konstantin and Bujotzek, Alexander and Weber, Marcus}, title = {A meshless discretization method for Markov state models applied to explicit water peptide folding simulations}, series = {Meshfree Methods for Partial Differential Equations VI}, volume = {89}, booktitle = {Meshfree Methods for Partial Differential Equations VI}, publisher = {Springer}, pages = {141 -- 154}, language = {en} } @misc{BujotzekSchuettNielsenetal., author = {Bujotzek, Alexander and Sch{\"u}tt, Ole and Nielsen, Adam and Fackeldey, Konstantin and Weber, Marcus}, title = {Efficient Conformational Analysis by Partition-of-Unity Coupling}, series = {Math Chem}, journal = {Math Chem}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42570}, abstract = {Obtaining a sufficient sampling of conformational space is a common problem in molecular simulation. We present the implementation of an umbrella-like adaptive sampling approach based on function-based meshless discretization of conformational space that is compatible with state of the art molecular dynamics code and that integrates an eigenvector-based clustering approach for conformational analysis and the computation of inter-conformational transition rates. The approach is applied to three example systems, namely n-pentane, alanine dipeptide, and a small synthetic host-guest system, the latter two including explicitly modeled solvent.}, language = {en} } @article{BujotzekSchuettNielsenetal., author = {Bujotzek, Alexander and Sch{\"u}tt, Ole and Nielsen, Adam and Fackeldey, Konstantin and Weber, Marcus}, title = {ZIBgridfree: Efficient Conformational Analysis by Partition-of-Unity Coupling}, series = {Journal of Mathematical Chemistry}, volume = {52}, journal = {Journal of Mathematical Chemistry}, number = {3}, doi = {10.1007/s10910-013-0265-1}, pages = {781 -- 804}, language = {de} }