速度跳跃过程：一种用于更快和更精确分子动力学模拟的多时间步方法的替代方法
Velocity jump processes : an alternative to multi-timestep methods for faster and accurate molecular dynamics simulations
摘要：
我们提出了一种新的路线，以加快分子动力学，通过使用速度跳跃过程，允许一个自适应的时间步长特定于每个原子-原子对（2体）的相互作用。我们首先介绍新的速度跳跃分子动力学的形式主义，遍历相对于典型的措施。然后，我们介绍了新的BOUNCE积分器，允许远程部队进行评估，在随机和最佳的时间步长，从而大大节省直接空间。第一个BOUNCE实现专用于经典（非极化）力场的准确性和计算性能进行测试的情况下，纯直接空间液滴样模拟和周期性边界条件（PBC）模拟使用光滑粒子网格埃瓦尔德。BOUNCE再现几个凝聚相性能的能力进行了分析。由于静电和范德华2体贡献的评估比使用1fs时间步长的标准积分器少得多，因此观察到高达400%的直接空间加速度。将可逆参考系传播子算法（BRONA（1））应用于倒易空间（多体）相互作用，使BOUNCE-BRONA（1）在PBC中保持较大的加速比，同时保持精度。总体而言，我们表明，取代BAOAB积分的BOUNCE自适应框架保留了类似的精度，并导致显着的计算节省。
英文摘要：
We propose a new route to accelerate molecular dynamics through the use of velocity jump processes allowing for an adaptive time-step specific to each atom-atom pair (2-body) interactions. We start by introducing the formalism of the new velocity jump molecular dynamics, ergodic with respect to the canonical measure. We then introduce the new BOUNCE integrator that allows for long-range forces to be evaluated at random and optimal time-steps, leading to strong savings in direct space. The accuracy and computational performances of a first BOUNCE implementation dedicated to classical (non-polarizable) force fields is tested in the cases of pure direct-space droplet-like simulations and of periodic boundary conditions (PBC) simulations using Smooth Particule Mesh Ewald. An analysis of the capability of BOUNCE to reproduce several condensed phase properties is provided. Since electrostatics and van der Waals 2-body contributions are evaluated much less often than with standard integrators using a 1fs timestep, up to a 400 % direct-space acceleration is observed. Applying the reversible reference system propagator algorithms (RESPA(1)) to reciprocal space (many-body) interactions allows BOUNCE-RESPA(1) to maintain large speedups in PBC while maintaining precision. Overall, we show that replacing the BAOAB integrator by the BOUNCE adaptive framework preserves a similar accuracy and leads to significant computational savings.
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