High Performance Molecular Dynamics

Wednesday, 28 September 2016 (All day) to Friday, 30 September 2016 (All day)

This course is in English. It is a PATC event.

Agenda

Slides

Description:

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.

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.
  • design a simulation project for a computing resource application.

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 UNIX and concepts of parallel computing.

Target: 
Companies
Research Institutions
Universities
Area: 
Science
Length: 
3 dd

Next courses

Any question?

For HPC and computer graphics courses, write to corsi.hpc@cineca.it

About CINECA

Cineca is a non profit Consortium, made up of 70 Italian universities, 5 Italian Research Institutions and the Italian Ministry of Education.

Today it is the largest Italian computing centre, one of the most important worldwide. With more seven hundred employees, it operates in the technological transfer sector through high performance scientific computing, the management and development of networks and web based services, and the development of complex information systems for treating large amounts of data.

It develops advanced Information Technology applications and services, acting like a trait-d'union between the academic world, the sphere of pure research and the world of industry and Public Administration. .

Visit the Cineca website