md2011-05-note_Part_10

md2011-05-note_Part_10 - I Velocity autocorrelation...

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Unformatted text preview: I Velocity autocorrelation function h v ( t ) v ( ) i can be used to calculate the chraracteristic vibrational states in a system. I Phonon density of states is simply g ( ) = Z d te i t h v ( t ) v ( ) i h v ( ) 2 i . (62) Notes O T MD S I Non-equilibrium MD (NEMD) methods is an envelope term to include all MD calculations not done in thermodynamic equilibrium. I Typically, a perturbative term is added to the equations of motion (or to the Hamiltonian), as briefly mentioned above. I There are special algorithms for studying, e.g., viscosity, heat conductivity and atomic diffusion. I In Brownian dynamics (or Langevin dynamics ) simulations, random forces are let to act on some atoms during the simulation. I The idea is to speed up infrequent events or to simulate effects of a non-interesting solvent (f.ex. on a protein). I Obviously, this makes the physical meaning of the atomic trajectories questionable....
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md2011-05-note_Part_10 - I Velocity autocorrelation...

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