Free energies and kinetic properties are essential for the quantitative characterization of the physical properties of various systems modelled using molecular simulations. Often times, however, the time-scales of the important biomolecular processes are much longer than the simulation lengths that can be currently afforded with the high-performance supercomputing resources. Novel computational approaches are thus needed to bridge this gap using improved algorithms.
This workshop will provide a hands-on introduction to two of the most successful enhanced-sampling methods that are widely used to compute the free energy landscape and the kinetics associated with complex biomolecular events. In days 1 and 2, we will introduce the theory and practicalities of Markov models, showing how they can be used to calculate free energies and kinetics from biased and unbiased molecular dynamics trajectories. In day 3, we will introduce the theory of Metadynamics-based enhanced sampling approaches, followed by step-by-step tutorials for setting up and analyzing metadynamics simulations with the open-source plug-in PLUMED.
The workshop is aimed at advanced PhD students or post-docs who already have a working knowledge of molecular dynamics simulations of bio-molecular systems. During the 3 day training, the participants will become familiar with the free open-source program packages and learn to effectively use them in their own research. The workshop is open to advanced PhD students, postdoctoral fellows, and principal investigators, including participants from industry. Participants will be encouraged to share their experience with rare events in biomolecular systems and to try and apply the acquired knowledge on their own systems.
In addition to tutorials and workshop materials, we will also host talks from industry representatives, including molecular modelling experts from Novartis and UCB Pharma.