Enhanced Sampling Methods Workshop

Enhanced Sampling Simulation Methods for Thermodynamics, Kinetics, and Pathways

Summary: How do ligands enter and leave buried binding sites? How do they diffuse through cell membranes? Where and what are the barriers that determine the kinetics? These are important questions that biomolecular simulations can offer unique insights into. But the timescales for these processes are often so slow that only enhanced sampling methods can make their study feasible. In this two-day workshop you will be introduced to a variety of enhanced sampling methods that can be used to predict pathways, kinetics and thermodynamics for a wide range of different problem types.

Day 1: Umbrella sampling, finite temperature string method, ligand unbinding simulations and machine learning-based analysis and CV identification.

Day2: Enhanced sampling with information bias for pathways and kinetics: the Weighted Ensemble method.

Pre-requisites: understanding classical MD simulations, basic python

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