Erik Lindahl

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Angle vibrations Similar to bonds: Should really be a QM oscillator, but can be approximated well Not quite as rigid as a bond, but almost
Torsions/dihedrals Frequently called “dihedral” angle too Angle between planes defined by atoms i-j-k Important! Gives rise to the & atoms j-k-l Ramachandran diagrams
Page 1: Protein Physics 2012 Lecture 2, Jan
Page 6 and 7: Natural amino acids
Page 9 and 10: α R β α L
Page 11 and 12: Outline today • More on interacti
Page 13 and 14: Semi-Empiric Modeling • Use simpl
Page 15: Bond stretching • Vibration aroun
Page 19 and 20: Nonbonded interactions Packing effe
Page 21 and 22: Lennard-Jones • Simpler form than
Page 23 and 24: Hydrophobic effect
Page 25: The Boltzmann Distribution ⇢ / e
Page 28 and 29: Formulating Boltzmann • Clapeyron
Page 30 and 31: Which shape is best energy-wise? Vo
Page 32 and 33: Free Energy • Use V=exp{ln(V)}
Page 34 and 35: How many states does this correspon
Page 36 and 37: Phase Transitions Explained • Sys
Page 38 and 39: Partitioning • Consider transfer

Erik Lindahl

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