Running a molecular dynamics simulation Minimize initial coordinates Assign random starting velocities from Maxwell-Boltzmann distribution 1/2 风() 2mhT/ exp/m,L 2kT Use small time step to integrate Newton's equations of motion (1 fs =1 x 10-15 sec is typical) Equilibration (running dynamics until system equilibrates) Production dynamics(useful dynamics at a desired tempRunning a Molecular Dynamics Simulation • Minimize initial coordinates • Assign random starting velocities from Maxwell-Boltzmann distribution 1/2 2 ⎞ p( vi) = ⎜ ⎛ mi ⎟ ⎞ exp⎜⎜ ⎛− mivi ⎟ ⎟ ⎝ 2 πkT ⎠ ⎝ 2kT ⎠ • Use small time step to integrate Newton’s equations of motion (1 fs =1 x 10-15 sec is typical) • Equilibration (running dynamics until system equilibrates) • Production dynamics (useful dynamics at a desired temp)