Multiscale Molecular Dynamics with MiMiC: Optimizing the Performance on Modern Supercomputers

With the emergence of exascale supercomputers comes the potential for new scientific breakthroughs in the simulation-driven fields, not least in the biomolecular domain. To efficiently exploit the vast resources offered by the complex hybrid CPU/GPU technologies present in modern supercomputers, requires careful attention to the setup and execution of the simulations. This is especially true for multiscale simulations that employ multiple programs with different performances and parallelization requirements.

This school targets early-career researchers with an interest in computational biochemistry and biophysics, but it is open to participants at all career stages from different computational fields. They will be trained on the efficient use of modern high-performance computing (HPC) facilities to solve problems in the field of computational biochemistry and biophysics using multiscale methods to model complex biomolecular systems, ranging from molecules in solution to membrane-embedded proteins. The large size of such systems and the long time scale of relevant phenomena necessitates the use of a combination of complementary techniques that allow spanning multiple temporal and spatial scales as well as the use of large-scale HPC facilities.

The participants will be taught advanced molecular dynamics (MD) simulation techniques for coupling multiple spatial resolutions using quantum mechanics/molecular mechanics (QM/MM) models and multiple time scales through multiple time step (MTS) algorithms, as well as the use of enhanced sampling methods.

Theoretical lectures will be complemented by practical sessions where the high-performance multiscale modeling framework MiMiC [6-9] will be used to run multiscale QM/MM MD simulations employing a variety of coupled external programs. These include CPMD, CP2K, and Quantum ESPRESSO together with GROMACS, OpenMM, and Tinker-HP for electrostatic- and polarizable-embedding QM/MM MD simulations based on density functional theory (DFT). The PLUMED library will be employed for enhanced-sampling and free-energy methods.

Throughout the school, a substantial emphasis will be placed on the crucial role of HPC in enabling efficient and accurate multiscale QM/MM simulations of large and complex biomolecular systems. This focus is closely connected with the MiMiC framework, which is designed to enable fast and highly parallelized multiscale MD simulations allowing to exploit modern heterogeneous supercomputing architectures.

More information will be available soon at this link.