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TOPICS DAYS.md

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TOPICS

Lecture 1/2: MD, forcefields, small molecules. Contents: Assumptions, timescales, limitations, well-known all-atom forcefields, criteria for selection.

Lecture 3/4: System building and hands-on. Contents: system building, equilibration workflows, small molecules in Amber, OpenMM, gelsolin as an example; hands-on with Colab + GPUs.

Lecture 5/6: MD analysis, and hands-on. Contents: motivation for gelsolin as an example system, AGel amyloidosis, crystallization of gelsolin G2+nanobody, G2/nanobody molecular models, simulation setup; hands-on with Colab and MDTraj.

Lecture 7/8: Advanced topics: Markovian models and Docking. Contents: Markov models for the analysis of biomolecules. State decomposition, timescales, training, convergence, equilibrium probabilities, free energies, kinetics, committors. Hands-on. Docking, redocking, pitfalls; hands-on on building and docking a toy library to COX-2.

DAY 1

Part 1 (~11,10-11,45)

  • MD, building, forcefields, small molecules

Part 2 (~12,00-12,40)

  • Amber build + run hands-on

Part 3 (~13,00-13,45)

  • OpenMM

Part 4 (~14,00-14,45)

  • OpenMM modeller build hands-on

DAY 2

Part 1 (~11,10-12,30?)

  • MD analysis with the GSN case + h.o.

Part 2 (~12,45-14,00?)

  • Markov state models + h.o.

Part 3 (~14,10-15,00?)

  • Docking + h.o.