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Methods for in-silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases. As these techniques become more complex and computationally costly we are faced with an increasing problem to provide a community of life-science researchers with a convenient way to run(More)
Particle swarm optimization (PSO) is a powerful technique for computer aided prediction of proteins' three-dimensional structure. In this work, employing an all-atom force field we demonstrate the efficiency of the standard PSO algorithm, as implemented in the ArFlock library, for finding the folded state of two proteins of different sizes starting from(More)
While the HPC community is working towards the development of the first Exaflop computer (expected around 2020), after reaching the Petaflop milestone in 2008 still only few HPC applications are able to fully exploit the capabilities of Petaflop systems. In this paper we argue that efforts for preparing HPC applications for Exascale should start before such(More)
Molecular simulation methods have increasingly contributed to our understanding of molecular and nanoscale systems. However, the family of Monte Carlo techniques has taken a backseat to molecular dynamics based methods, which is also reflected in the number of available simulation packages. Here, we report the development of a generic, versatile simulation(More)
The numerical efficiency of different schemes for solving the Liouville-von Neumann equation within multilevel Redfield theory has been studied. Among the tested algorithms are the well-known Runge-Kutta scheme in two different implementations as well as methods especially developed for time propagation: the Short Iterative Arnoldi, Chebyshev and Newtonian(More)
Particle swarm optimization is a powerful technique for computer aided prediction of proteins’ three-dimensional structure. In this work, employing an all-atom force field and the standard algorithm, as implemented in the ArFlock library in previous work, the low-energy conformations of several peptides of different sizes in vacuum starting from completely(More)
Opus IB is an Opteron based cluster system with InfiniBand interconnect. Grid middleware provide the integration into CampusGrid and D-Grid projects. Mentionable details of hardware and software equipment as well as configuration of the cluster will be introduced. Performance measurements show that InfiniBand is not only well suited for message-passing(More)
Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise requires prior specific permission by the publisher mentioned above. A(More)
In this paper we propose an approach for preparing HPC applications for Exascale. A high-level application model capturing non-functional properties combined with an abstract machine model will enable application improvements, and will serve as input to runtime systems to handle performance and energy optimizations, and self-aware fault management. A(More)