Parallel biomolecular simulation: Theory, algorithms and implementation

The essential goal of this work is the unified treatment of quantum mechanical and classical degrees of freedom in biomolecular simulation on all three levels: Theory, algorithms and implementation. In theory this is done within the framework of the Lagrangian model, which handles electronic coordinates and Cartesian nuclear coordinates in a consistent way. Furthermore, there is a 1:l correspondence between the various algorithmic substeps of selfconsistent-force molecular dynamics (SCF-MD) and classical molecular dynamics (CMD): The overlap criterion corresponds to the cut-off principle, the list of integrals to the pairlist and the computation of interaction matrix elements to the computation of pair forces. (The integration step is identical in both schemes.) This complete analogy can be conserved on the implementation level, for which actual benchmarks on three common architectures are given for a CMD simulation of the hydrated protein ubiquitin.