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.
The course will consist of presentations and practical sessions where students will be able to prepare and run examples of popular programs such as GROMACS and NAMD on the supercomputers of Cineca.
By the end of the course each student should be able to:
- comprehend the basic principles of classical molecular dynamics (MD).
- understand the common algorithms for the optimization and parallelization of MD applications and the factors limiting the performance and parallel scaling.
- run and optimize MD simulations on advanced, multicore architectures equipped with both conventional processors and accelerators such as NVIDIA GPUs.
- design a simulation project for a computing 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.