Summary
- Principal component analysis
- diagonalization of covariance matrix
- yields low dimensional description of predominant
collective fluctuations
- can be used on any (sub)set of structures/coordinates
- useful for the comparison of different ensembles
- can be used to drive subsequent simulations
(essential dynamics/flooding)
- Normal Mode analysis
- Taylor expansion of potential energy to second order
- Harmonic approximation of one (local) minimum
- full thermodynamic picture (enthalpy, entropy)
- conformational transitions largely anharmonic
- solvent not easily included