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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.
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.