In this talk a short review of molecular dynamics simulations of biomolecules will be first given. Then, a widely used numerical iterative scheme for constrained molecular dynamics simulations, SHAKE, is described and analyzed in a general algorithmic framework. Further, based on this general algorithmic framework, an accelerated variant of SHAKE, called SHAKE-SOR, is introduced and analyzed. Finally, numerical results for three biomolecules (two proteins and one DNA) will be presented to show that SHAKE-SOR can significantly improve the performance of standard SHAKE by reducing the number of iterations per timestep.

WHERE: TEC 251