Erik Lindahl

More documents

Recommendations

Info

van der Waals interactions • Atoms repel each other at close distance due to overlap of electrons (repulsion) • All atoms attrach each other at long distance due to induced dipole effects (dispersion) Example - Buckingham potential: V (r)=Aexp Br + C 6 r 6 Same problem as before: exp(r) is slow to calculate
Lennard-Jones • Simpler form than Buckingham • In practice, atoms should never approach really close, so we just want a basic model of the repulsion • Smart trick: When we have calculated 1/r 6 , it is trivial to get 1/r 12 (1 multiplication) • Lennard-Jones potential V (r)= N Â i=1 N Â j=1 C 12 r 12 ij C 6 r 6 ij !
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 and 16: Bond stretching • Vibration aroun
Page 17 and 18: Torsions/dihedrals Frequently calle
Page 19: Nonbonded interactions Packing effe
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

Create successful ePaper yourself

Delete template?

Save as template?