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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