Analysis of the SHAKE-SOR Algorithm for Constrained Molecular Dynamics Simulations
Molecular dynamics integration with bonds constrained to equilibrium values
is a common approach used to increase the feasible timestep and hence
reduce the overall simulation time. Here we analyze
the widely used numerical iterative scheme
for constrained molecular dynamics simulations, SHAKE, in a
general algorithmic framework, from which SHAKE's relationship to
nonlinear solvers can be established. Using
the nonlinear SOR-Newton iterative method, we define an accelerated variant
of SHAKE, called SHAKE-SOR, and prove a fundamental relationship
between SHAKE-SOR and SOR-Newton. Based on this relationship, the
convergence of SHAKE-SOR is proved in the
framework of nonlinear SOR theory. Numerical results show that SHAKE-SOR
can significantly improve the performance of standard SHAKE by reducing
the number of iterations per timestep through an optimal parameter choice.
Submitted to a special issue of Methods and Applications of Analysis dedicated to Prof. Cathleen Morawetz of the Courant Institute
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