Praprotnik Matej, Janezic Dusanka
National Institute of Chemistry, Ljubljana, Slovenia.
J Chem Phys. 2005 May 1;122(17):174103. doi: 10.1063/1.1884609.
The new symplectic molecular dynamics (MD) integrators presented in the first paper of this series were applied to perform MD simulations of water. The physical properties of a system of flexible TIP3P water molecules computed by the new integrators, such as diffusion coefficients, orientation correlation times, and infrared (IR) spectra, are in good agreement with results obtained by the standard method. The comparison between the new integrators' and the standard method's integration time step sizes indicates that the resulting algorithm allows a 3.0 fs long integration time step as opposed to the standard leap-frog Verlet method, a sixfold simulation speed-up. The accuracy of the method was confirmed, in particular, by computing the IR spectrum of water in which no blueshifting of the stretching normal mode frequencies is observed as occurs with the standard method.
本系列第一篇论文中提出的新型辛分子动力学（MD）积分器被应用于水的MD模拟。通过新型积分器计算得到的柔性TIP3P水分子系统的物理性质，如扩散系数、取向相关时间和红外（IR）光谱，与标准方法得到的结果吻合良好。新型积分器与标准方法的积分时间步长比较表明，由此产生的算法允许使用3.0飞秒的长积分时间步长，而标准的蛙跳Verlet方法则不行，模拟速度提高了六倍。特别是通过计算水的红外光谱证实了该方法的准确性，在该光谱中未观察到标准方法中出现的拉伸正常模式频率的蓝移。
