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.
Scientists with research interests in classical molecular dynamics in computational biology, chemistry or biophysics.
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.
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.
Andrew Emerson (Cineca)
Giovanni Chillemi (Cineca)
Alessandro Grottesi (Cineca)