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Sunday, 17 March (Day 1) [15:00-18:00]
Sunday, 17 March (Day 1) [15:00-18:00]
Theory: Free Energy from molecular dynamics simulations: Basics, theoretical framework, analytical model systems, Issues with sampling problems.
Monday, 18 March (Day 2) [09:00-18:00]
Monday, 18 March (Day 2) [09:00-18:00]
Theory: Free energy from global tempering methods: Parallel tempering, Hamiltonian replica exchange, other novel global tempering techniques.
Practicals: Free energy calculations of model system systems, small molecular systems using GROMACS, PIMD
Tuesday, 19 March (Day 3) [09:00-18:00]
Tuesday, 19 March (Day 3) [09:00-18:00]
Theory: Free energy calculations using alchemical methods, novel developments in this field, and applications to various problems (drug binding, pKa etc.)
Practicals: Free energy differences between simple molecules, drug binding, pKa calculation
Wednesday, 20 March (Day 4) [09:00-18:00]
Wednesday, 20 March (Day 4) [09:00-18:00]
Theory: Free energy calculations using collective variables: umbrella sampling, blue-moon ensemble
Practicals: conformational changes, drug binding, protein folding, comparison of methods
Thursday, 21 March (Day 5) [15:00-18:00]
Thursday, 21 March (Day 5) [15:00-18:00]
Theory: metadynamics, temperature accelerated molecular dynamics and new methods like parallel-bias metadynamics, temperature accelerated sliced sampling
Friday, 22 March (Day 6) [09:00-18:00]
Friday, 22 March (Day 6) [09:00-18:00]
Theory: Testing collective variables, transition path sampling, sampling reaction pathways, computation of rates
Practicals: conformational changes, drug binding, protein folding, comparison of methods
Saturday, 23 March (Day 7)
Saturday, 23 March (Day 7)
Departure after breakfast
Suggested Readings
Suggested Readings
- Statistical Mechanics: Theory and Molecular Simulation by Mark E. Tuckerman
- Reaction Rate Theory and Rare Events by Baron Peters
- Free Energy Calculations by Christophe Chipot & Andrew Pohorille
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