Sampling the Potential Energy Surface Energy minimization downhill search, generally to nearest local minimum can be used to relax structures might be useful to define local changes due to mutation Normal mode analysis defines "characteristic motions which are distortions about a local minimum structure orders motions "easy(low frequency to hard"(high) Molecular dynamics movie of motion at given temperature (300 k) equivalent to statistical mechanical ensemble Monte Carlo/ simulated Annealing Describe properties of the landscape and thermodyanmic parameters without simulating how the molecular actually movesSampling the Potential Energy Surface • Energy minimization – “downhill” search, generally to nearest local minimum – can be used to relax structures – might be useful to define local changes due to mutation • Normal mode analysis – defines “characteristic motions”, which are distortions about a local minimum structure – orders motions “easy” (low frequency) to “hard” (high) • Molecular dynamics – movie of motion at given temperature (300 K) – equivalent to statistical mechanical ensemble • Monte Carlo/Simulated Annealing – Describe properties of the landscape and thermodyanmic parameters without simulating how the molecular actually moves