Baker Katherine, Baumketner Andrij, Lin Yuchun, Deng Shaozhong, Jacobs Donald, Cai Wei
Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, NC 28223, United States.
Comput Phys Commun. 2013 Jan 1;184(1):19-26. doi: 10.1016/j.cpc.2012.08.003. Epub 2012 Aug 14.
We present an order N method for calculating electrostatic interactions that has been integrated into the molecular dynamics portion of the TINKER Molecular Modeling package. This method, introduced in a previous paper [J. Chem. Phys. 131 (2009) 154103] and termed the Image-Charge Solvation Model (ICSM), is a hybrid electrostatic approach that combines the strengths of both explicit and implicit representations of the solvent. A multiple-image method is used to calculate reaction fields due to the implicit part while the Fast Multipole Method (FMM) is used to calculate the Coulomb interactions for all charges, including the explicit part. The integrated package is validated through test simulations of liquid water. The results are compared with those obtained by the Particle Mesh Ewald (PME) method that is built in the TINKER package. Timing performance of TINKER with the integrated ICSM is benchmarked on bulk water as a function of the size of the system. In particular, timing analysis results show that the ICSM outperforms the PME for sufficiently large systems with the break-even point at around 30,000 particles in the simulated system.
我们提出了一种用于计算静电相互作用的N阶方法，该方法已被集成到TINKER分子建模软件包的分子动力学部分。这种方法在之前的一篇论文[《化学物理杂志》131 (2009) 154103]中被提出，称为镜像电荷溶剂化模型(ICSM)，是一种混合静电方法，它结合了溶剂显式表示和隐式表示的优点。使用多重镜像方法计算隐式部分产生的反应场，而使用快速多极子方法(FMM)计算所有电荷的库仑相互作用，包括显式部分。通过对液态水的测试模拟验证了该集成软件包。将结果与TINKER软件包中内置的粒子网格埃瓦尔德(PME)方法得到的结果进行比较。以体水为研究对象，对集成了ICSM的TINKER的计时性能进行了基准测试，测试结果是系统大小的函数。特别是，计时分析结果表明，对于足够大的系统，ICSM的性能优于PME，在模拟系统中，盈亏平衡点约为30,000个粒子。
