Cerutti David S, Duke Robert E, Darden Thomas A, Lybrand Terry P
Center for Structural Biology, Department of Chemistry, Vanderbilt University 5142 Medical Research Building III, 465 21st Avenue South, Nashville, TN 37232-8725.
J Chem Theory Comput. 2009 Sep 8;5(9):2322. doi: 10.1021/ct9001015.
We draw on an old technique for improving the accuracy of mesh-based field calculations to extend the popular Smooth Particle Mesh Ewald (SPME) algorithm as the Staggered Mesh Ewald (StME) algorithm. StME improves the accuracy of computed forces by up to 1.2 orders of magnitude and also reduces the drift in system momentum inherent in the SPME method by averaging the results of two separate reciprocal space calculations. StME can use charge mesh spacings roughly 1.5× larger than SPME to obtain comparable levels of accuracy; the one mesh in an SPME calculation can therefore be replaced with two separate meshes, each less than one third of the original size. Coarsening the charge mesh can be balanced with reductions in the direct space cutoff to optimize performance: the efficiency of StME rivals or exceeds that of SPME calculations with similarly optimized parameters. StME may also offer advantages for parallel molecular dynamics simulations because it permits the use of coarser meshes without requiring higher orders of charge interpolation and also because the two reciprocal space calculations can be run independently if that is most suitable for the machine architecture. We are planning other improvements to the standard SPME algorithm, and anticipate that StME will work synergistically will all of them to dramatically improve the efficiency and parallel scaling of molecular simulations.
我们借鉴一种用于提高基于网格的场计算精度的旧技术，将流行的光滑粒子网格埃瓦尔德（SPME）算法扩展为交错网格埃瓦尔德（StME）算法。StME将计算力的精度提高了多达1.2个数量级，并且通过对两个单独的倒易空间计算结果进行平均，还减少了SPME方法中固有的系统动量漂移。StME可以使用比SPME大1.5倍左右的电荷网格间距来获得相当的精度水平；因此，SPME计算中的一个网格可以被两个单独的网格取代，每个网格的大小都小于原始大小的三分之一。电荷网格的粗化可以通过减小实空间截止来平衡，以优化性能：StME的效率与具有类似优化参数的SPME计算相当或更高。StME对于并行分子动力学模拟也可能具有优势，因为它允许使用更粗的网格，而无需更高阶的电荷插值，并且如果这最适合机器架构，两个倒易空间计算可以独立运行。我们正在计划对标准SPME算法进行其他改进，并预计StME将与所有这些改进协同工作，以显著提高分子模拟的效率和并行扩展性。
