Paper Citing NAMD - Abstract
Cerutti, David S.; Duke, Robert E.; Darden, Thomas A.; Lybrand, Terry P.
Staggered Mesh Ewald: An Extension of the Smooth Particle-Mesh Ewald Method Adding Great Versatility
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2322-2338, SEP 2009
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 x 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.
