Implementation of Particle-Mesh Ewald(PME) on Graphics Processing Units

In this article,long range part of electrostatic interaction is accelerated using GPUs in NIVIDIA CUDA programming environment.Particle Mesh Ewald algorithm is adopted and split into 5 procedures:parameters designation,discretization of point charges into grids,Fourier transformation of grids,potential of electrostatic interaction,and force calculation of electrostatic interaction.The codes are tested by seven biomolecular systems with different sizes.Roughly 7-fold speedup over one core of mainstream CPUs is obtained.The codes can be integrated into molecular dynamic simulation software packages that already exst or used as part of GPU codes developed in the future to further speedup traditional MD simulations.