Description:

This course is designed for those users who wish run classical molecular dynamics programs 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.
During the course students will be guided on how to prepare and run simulations on Cineca's HPC systems with the GROMACS application,
one of the most common and efficient molecular dynamics applications available.

Skills:

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.
• perform advanced data analysis of the simulation results with Gromacs and Python tools
• design a simulation project for a computing resource application.
• launch simulations with the metadynamics method to enhance the sampling of rare events and free energy landscape

Target Audience:

Scientists with research interests in classical molecular dynamics in computational biology, chemistry or biophysics.

Pre-requisites:

Research interest in classical molecular dynamics with a focus on the simulation of biomolecular systems. Basic knowledge of Linux with the ability to edit files in a UNIX shell environment. Knowledge of Python and Python libraries, especially Numpy and Pandas, would also be beneficial. We recommend that participants follow some online tutorials prior to the course.