This course is designed for those users who wish run classical molecular dynamics programs such as GROMACS and NAMD on modern supercomputers. By understanding better the HPC infrastructures and the algorithms used to exploit them, the aim is to give researchers the tools to run simulations in the most efficient way possible on current and future supercomputers.
At least half the course will be devoted to practical sessions where students will be able to prepare and run GROMACS or NAMD examples on the supercomputers of Cineca.
Basic principles of classical Molecular Dynamics (MD). Common algorithms for the optimization and parallelization of MD applications and factors limiting the performance and parallel scaling. Application of MD on multi-core and hybrid architectures equipped with accelerators such as Intel Xeon PHIs. Project design and strategies for resource application.
Scientists with research interests in classical molecular dynamics in computational biology, chemistry or biophysics.
Research interest in classical molecular dynamics with a focus on the simulation of biomolecular systems. Basic knowledge of UNIX and concepts of parallel computing.