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Million-core Molecular Simulation

Final Report Summary - MEGASIM (Million-core Molecular Simulation)

Since a decade, clock frequencies of computer processors no longer increase significantly. Moore's law, however, still holds. So instead of getting faster processors we get more and more cores. For so called "weak scaling" problems, were one can scale the problem size, this is not a fundamental issue. But for "strong scaling" problems, such as molecular dynamics simulations, this is problematic. As the problem size is fixed, but the CPU and GPU core count continuously increases, we need to make the computational software scale better and better. That was one of the main goals of this project. We have transformed the GROMACS open source molecular simulation package from running only on CPUs with message-passing parallelization to a state-of-the-art hybrid MPI-thread parallelization and hybrid CPU-GPU accelerated code. GROMACS is now likely the fastest parallel package in the world and can scale to millions of CUDA GPU cores. Furthermore, the algorithms developed are flexible and can easily be adapted to new hardware when it is released.

Two applications areas were part of this project. One is biomolecular simulation. MD is used to study e.g. proteins and DNA to understand diseases and help develop new drugs. Conformational transitions are central in the function of many biomolecules, but these are often on the order of milliseconds, whereas MD can currently reach microseconds. We have developed the Accelerated Weight Histogram method, which provides exponential acceleration of free-energy barriers along such transitions. This puts many conformational transitions within reach of MD simulations. A second application area is wetting of substrates by (water) droplets. Although droplets are large compared to the molecular scale of a nanometer, the particle nature of the liquid plays an important role. This is especially clear at the contact line, where substrate, water and air meet. Water does not slip over a hydrophilic substrate, which poses a problem for continuum hydrodynamics. We have studies this using molecular dynamics simulations with droplets consisting of millions of atoms. The contact line advanced by individual water molecules hydrogen bonding to the substrate ahead of the contact line. During this process a lot of energy is dissipated, which account for half of the total energy dissipation during wetting. Thus events in a region narrower than a nanometer affect the dynamics on millimeter length scales.