Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
J Chem Phys. 2020 Dec 21;153(23):234115. doi: 10.1063/5.0027873.
Recently, we proposed novel temperature and pressure evaluations in molecular dynamics (MD) simulations to preserve the accuracy up to the third order of a time step, δt [J. Jung, C. Kobayashi, and Y. Sugita, J. Chem. Theory Comput. 15, 84-94 (2019); J. Jung, C. Kobayashi, and Y. Sugita, J. Chem. Phys. 148, 164109 (2018)]. These approaches allow us to extend δt of MD simulations under an isothermal-isobaric condition up to 5 fs with a velocity Verlet integrator. Here, we further improve the isothermal-isobaric MD integration by introducing the group-based evaluations of system temperature and pressure to our previous approach. The group-based scheme increases the accuracy even using inaccurate temperature and pressure evaluations by neglecting the high-frequency vibrational motions of hydrogen atoms. It also improves the overall performance by avoiding iterations in thermostat and barostat updates and by allowing a multiple time step integration such as r-RESPA (reversible reference system propagation algorithm) with our proposed high-precision evaluations of temperature and pressure. Now, the improved integration scheme conserves physical properties of lipid bilayer systems up to δt = 5 fs with velocity Verlet as well as δt = 3.5 fs for fast motions in r-RESPA, respectively.
最近，我们提出了新的温度和压力评估方法，用于分子动力学（MD）模拟，以在时间步长 δt 下保持三阶精度[J. Jung、C. Kobayashi 和 Y. Sugita，J. Chem. Theory Comput. 15，84-94（2019）；J. Jung、C. Kobayashi 和 Y. Sugita，J. Chem. Phys. 148，164109（2018）]。这些方法允许我们在等压等温和速度-Verlet 积分器下将 MD 模拟的 δt 扩展到 5fs。在这里，我们通过将系统温度和压力的分组评估引入到我们之前的方法中，进一步改进了等压等温和 MD 积分。分组方案通过忽略氢原子的高频振动运动，即使在不准确的温度和压力评估下，也能提高精度。它还通过避免在恒温器和恒压器更新中的迭代，以及允许使用我们提出的高精度温度和压力评估的 r-RESPA（可逆参考系统传播算法）等多个时间步长积分，提高了整体性能。现在，改进的积分方案可以使用速度-Verlet 将脂质双层系统的物理性质保持到 δt = 5fs，并且在 r-RESPA 中对于快速运动可以保持到 δt = 3.5fs。
