BEMOLPA: Beschleunigung von Molekuelmechanik-Programmen durch neue parallele Algorithmen. Komplexitaetsreduzierung und Parallelisierung eines MD-Algorithmus Abschlussbericht

Key issue of the project was to generate a computer code (MEGADYN) for the simulation of molecular dynamics of large simulation ensembles (up to 10"6 atoms) on the basis of classical force-field models. A reduction of complexity of the calculation of forces and energy down to O(N) was achieved by employing the fast multiple method FMM to the Coulomb interaction. Special care was taken of periodic boundary conditions. Within the framework of FMM they were realized in a minimum image convention-type manner. Thus, MEGADYN can be used to simulate NVT-, as well as NPT-ensembles. Time integration of Newton's equation of motion is performed by a Verlet-algorithm in a leap-frog version. For future applications in the area of biomembranes, the possibility for special anisotropic periodic boundary conditions has been incorporated. On parallelization of MEGADYN processor communication has been organized partly in star-type topology, partly in a ring-type topology. Common message passing systems like PVM, POE, or systems based on the MPI standard can be used. Several simulations of systems up to 540.000 atoms have been run successfully. Systems with 1.000.000 atoms can be simulated with reasonable amounts of computer time. MEGADYN can be run on distributed (IBM-SP2, 32 processors), as well as shared memory computer systems (Silicon Graphics Power Challenge, 16 processors). Speed-up factors are close to the number of processors. (orig.)Available from TIB Hannover: DtF QN1(40,44) / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekSIGLEBundesministerium fuer Bildung, Wissenschaft, Forschung und Technologie, Bonn (Germany)DEGerman