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CECAM Tutorial "Atomistic Monte Carlo Simulations of Bio-molecular Systems"

The CECAM tutorial "Atomistic Monte Carlo Simulations of Bio-molecular Systems" took place at JSC from 15 to 19 September 2014 and was attended by 25 scientists from seven countries. The tutorial featured a range of lessons and hands-on practical sessions to provide scientists with everything necessary to apply this technique to their own research topics.

After an intensive introduction to the theoretical foundations of Monte Carlo (MC) simulations by Prof. Anders Irbäck (Lund University), the participants consolidated their knowledge in the hands-on sessions using the open source MC simulation package ProFASi. This software is under active development at the Simulation Laboratory Biology at JSC. The participants learned to set up, monitor, and analyse MC simulations with ProFASi on the HPC resources of JSC. The exercises introduced scientifically interesting all-atom protein folding and aggregation simulations. Such processes are often too slow to be simulated by classical molecular dynamics, and the tutorial presented MC as a powerful alternative tool. Wouter Boomsma (University of Copenhagen) showed how to integrate available experimental information with the MC sampling procedure as an advanced application. Finally, the programming interface of ProFASi was introduced to encourage research and experimentation with new MC techniques. The CECAM tutorial concluded with some recent research highlights using atomistic MC simulations, and a lively discussion of best practices and future developments with the participants.

Overall, it proved to be a significant community-building event for the ProFASi software package, and provided much stimulus for future development work by the SimLab Biology.
(Contact: Dr. Sandipan Mohanty,