Long-Timestep Biomolecular Dynamics Simulations:
LN Performance on a Polymerase ß / DNA System
Multiple-timestep (MTS) integrators for biomolecular simulations
are promising approaches for enhancing computational efficiency.
To overcome resonance limitations on the outer timestep size,
nonsymplectic variants can be used.
A Langevin/MTS algorithm termed LN based on extrapolative force splitting
is described that alleviates these resonance artifacts and allows larger
timesteps. LN performance is detailed on
a large biomolecular system of 45,000 atoms in terms of energetics,
dynamics, and geometry. These results show good reproduction of small-timestep
trajectories and substantial computational gains.
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