High Performance Molecular Dynamics@CINECA



Via Magnanelli, 6/3, 40033 Casalecchio di Reno BO ITALY


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.
  • Target Audience:
  • 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.


A grant of 300 EUR (for foreign students) and 150 EUR (for Italian students) will be available for participants not funded by their institution and not working in the Bologna area.
Some documentation will be required and the grant will be paid only after a certified presence of minimum 80% of the lessons and about 1 month after the ending of the course.
For further information about how to submit for the grant, please wait the confirmation email that you are accepted to the course about 3 weeks before the date of the beginning of the lessons. 

The lunch for the 3 days will be provided by Cineca.

Coordinating Teacher: Dr. Andrew Emerson

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