CECAM School: Atomistic Monte Carlo Simulations of Bio-molecular Systems
Sandipan Mohanty
This event will take place as an on-site and in-person event. It is not possible to attend online.
Practical all-atom protein folding simulation using Monte Carlo
Molecular simulation is currently dominated by molecular dynamics (MD). The surge in available computational power on current supercomputers has extended the reach of MD simulations considerably, but the time scales that are relevant for many biological processes are still often orders of magnitude longer than what can currently be covered by all-atom MD. Markov Chain Monte Carlo (MCMC) simulations, grounded in the principles of statistical physics and stochastic sampling, offer an interesting ensemble-based alternative.
Coarse grained representations are another way to overcome these limitations, but reproduce some properties of such processes only approximately. All-atom representations remain essential for an in-depth understanding of phenomena, such as protein folding, that emerge from a network of atomic-scale interactions. Ensemble techniques like MCMC have demonstrated that unbiased all-atom simulations of non-trivial proteins are feasible.
Using MCMC as an effective tool in biophysical research requires an understanding of the similarities and differences between MCMC and MD with respect to techniques and suitability for different scientific questions.
We therefore invite you to attend the Centre Européen de Calcul Atomique et Moléculaire (CECAM) school "Atomistic Monte Carlo Simulations of Bio-molecular Systems" which highlights the possibilities of all-atom MCMC simulations and introduces ProFASi, an open source high performance software for MCMC simulation of proteins.
In this one-week CECAM school, taking place at the Jülich Supercomputing Centre from 22 to 26 September you will:
- Understand the principles of MCMC simulations and how they compare to MD simulations
- Perform unbiased protein folding simulations on a supercomputer yourself
- Generate and analyse free energy landscapes of protein folding and learn how to interpret them
- Perform different Monte Carlo techniques and learn when and how to apply them
- Practice parametrising, monitoring, and optimising Monte Carlo simulations
- Get an overview of the ProFASi software, its tools, and its easy customisation via plugins
- Discuss pros and cons of different simulation approaches as well as your own use cases
Prerequisites:
A basic understanding of molecular simulation of proteins. A basic understanding of Linux commands, Jupyter notebooks and Python is helpful.
Target Audience:
Everyone with a basic knowledge of biomolecular simulation
Language:
The CECAM school will be held in English.
Dates:
22-26 September 2025, 09:00-17:30
Venue:
Jülich Supercomputing Centre, Building 14.14, BR 6
Number of Participants:
Maximum 18
Instructors:
Jan Meinke, Sandipan Mohanty, Olav Zimmermann
There are no course fees. Travel and accommodation need to be organised and paid by the participant. Unfortunately we cannot provide any travel grants.
The course is organised by the Simulation and Data Laboratory Biology at JSC.
Applications are only possible via the CECAM page:
https://www.cecam.org/workshop-details/atomistic-monte-carlo-simulations-of-bio-molecular-systems-1401
Deadline: August 22, 2025
Contact:
- Institute for Advanced Simulation (IAS)
- Jülich Supercomputing Centre (JSC)
Room 4011