Increasing the Time Step and Efficiency of Molecular Dynamics Simulations: Optimal Solutions for Equilibrium Simulations or Structure Refinement of Large Biomolecules
作者： Urs Stocker , Daniel Juchli , Wilfred F. van Gunsteren
DOI: 10.1080/0892702031000065791
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摘要: In biomolecular simulation, the different force field terms determine motional frequencies found in a particular simulation. By eliminating high frequencies, longer time steps can be achieved equilibrium and refinement (non-equilibrium) simulations, sometimes at expense of decreasing physical correctness simulated system. The used molecular simulations constrained or softened leading to maximum step 5 fs for which static properties are not affected by changes parameters introduced, but dynamical quantities are. Using very smoothed, soft interaction function increased hydrogen masses, 14 reached. However, it should only unphysical dynamics minor importance.
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