论文标题
速度跳跃过程:用于更快,准确的分子动力学仿真的多动蛋白方法的替代方法
Velocity jump processes : an alternative to multi-timestep methods for faster and accurate molecular dynamics simulations
论文作者
论文摘要
我们通过使用速度跳跃过程,提出了一种新的途径来加速分子动力学,从而允许每个原子原子对(2型)相互作用具有适应性的时间步长。我们首先引入新速度跳跃分子动力学的形式,相对于规范度量。然后,我们介绍了新的Bounce积分器,该集成器允许以随机和最佳的时间步长评估远程力量,从而在直接空间中节省大量。在使用平滑的颗粒网状ewald的纯直接空间液滴模拟和周期性边界条件(PBC)模拟的情况下,测试了专用于经典(不可极化)力场的首次反弹实现的准确性和计算性能。提供了反弹重现几种凝结相性能的能力的分析。由于静电和范德华2体贡献的评估频率远低于使用1FS时间段的标准积分器的频率,因此观察到高达400%的直接空间加速度。将可逆的参考系统传播算法(Respa(1))应用于倒数空间(多体)相互作用允许Bounce-Respa(1)在保持精度的同时维持PBC中的较大加速。总体而言,我们表明,通过反弹自适应框架代替BAOAB集成器可以保持相似的精度,并导致大量的计算节省。
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.