Molecular Dynamics Simulations Simulate motions of molecules as a function of time Collect short movie"of protein"swimming"in solution Can use the simulation to compute Average structure( at given temperature, 7) Atomic fluctuations (at 7) Thermodynamic quantities(temperature dependent) 声, (t+a)=r()+n(t+c/2) (t+/2)=v(t-/2)+( Verlet leap frog algorithmMolecular Dynamics Simulations • Simulate motions of molecules as a function of time – Collect short “movie” of protein “swimming” in solution • Can use the simulation to compute: – Average structure (at given temperature, T) – Atomic fluctuations (at T) – Thermodynamic quantities (temperature dependent) m ∂ 2 xi Fi Fi = mi ai ai = = − ∇iU i ∂ t2 mi G G r (t + δt) = r ( t) + δ G tv t ( + δt /2) G v (t + δt /2) = G v (t − δt /2) + δt G a ( t) Verlet “leap frog” algorithm