Computer engineering of complex physical and chemical systems by Parallel Molecular Dynamics computations
Parallel Molecular Dynamics (PMD) of complex systems are based on different PVM strategies depending on the nature of the complex system. Two different examples of PMD by PVM will be given. The first example is a simulation, on sp2, of a phase separation in a binary mixture of 343 000 molecules which takes place within millions of time steps. This (physical) system is suitable for a domain decomposition PVM-strategy. The second example is the simulation of an active enzyme in different solvents. The (chemical) system is complex by its nature with many different chemical compounds and suitable for a PVM particle decomposition.
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