@misc{KrauseFackeldeyKrause, author = {Krause, Dorian and Fackeldey, Konstantin and Krause, Rolf}, title = {A parallel multiscale simulation toolbox for coupling molecular dynamics and finite elements}, issn = {1438-0064}, doi = {10.1007/978-3-319-00786-1_14}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42354}, abstract = {It is the ultimate goal of concurrent multiscale methods to provide computational tools that allow to simulation physical processes with the accuracy of micro-scale and the computational speed of macro-scale models. As a matter of fact, the efficient and scalable implementation of concurrent multiscale methods on clusters and supercomputers is a complicated endeavor. In this article we present the parallel multiscale simulation tool MACI which has been designed for efficient coupling between molecular dynamics and finite element codes. We propose a specification for a thin yet versatile interface for the coupling of molecular dynamics and finite element codes in a modular fashion. Further we discuss the parallelization strategy pursued in MACI, in particular, focusing on the parallel assembly of transfer operators and their efficient execution.}, 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} }