Parallel Biomolecular Simulation: An Overview and Analysis of Important Algorithms

摘要

Molecular Dynamics (MD) delivers dynamical information for large biomolecular systems - using enormous CPU-resources. Consequently, several implementations of parallel MD programs have been presented.~(1-13) We will analyse the characteristics of MD simulations of real-live biomolecular systems, summarise the serial algorithms that have been developed to significantly speed up these simulations and take a look at the fitness of these algorithms for parallelisation.