High Performance Molecular Dynamics

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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.

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.

Research Institutions
3 dd
Minimum number of attendants required: 

Next courses

Non sono previste edizioni di questo corso.

Any question?

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


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