title: Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systems.
abstract: Isotropic periodic sum (IPS) is a method for the calculation of long-range interactions in molecular simulation based on the homogeneity of simulation systems. Three IPS models, 3D IPS, 2D IPS, and 1D IPS have been developed for three common types of homogeneous systems. Based on the fact that 3D IPS can well describe the long-range interactions of a heterogeneous system if a local region larger than the homogeneity scale is used, this work presents a method based on 3D IPS to calculate long-range interactions for all kinds of simulation systems, including homogeneous, heterogeneous, and finite systems. Unlike the original 3D IPS method that uses a local region defined by the cutoff distance, this method uses a local region larger than that defined by the cutoff distance to reach the homogeneity scale. To efficiently calculate interactions within such a large local region, this method split long-range interactions into two parts, a cutoff part and a long-range part. The cutoff part is calculated by summing over atom pairs within a cutoff range (about 10 A), and the long-range part is calculated using the discrete fast Fourier transform (DFFT) technique. This method is applied to electrostatic and van der Waals interactions for both periodic and non-periodic systems. Example simulations demonstrate that this method can accurately and efficiently calculate long-range interactions for molecular simulation.
authors.affiliation: Laboratory of Computational Biology, NHLBI, NIH, Bethesda, Maryland 20892, USA. wuxw@nhlbi.nih.gov
authors.forename: Xiongwu
authors.initials: X
authors.lastname: Wu
authors.forename: Bernard R
authors.initials: BR
authors.lastname: Brooks
mesh_terms: D000465:Algorithms; D002352:Carrier Proteins / Q000737:chemistry; D005583:Fourier Analysis; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D012680:Sensitivity and Specificity; D012964:Sodium / Q000737:chemistry; D013500:Surface Tension; D014618:Vacuum; D014867:Water / Q000737:chemistry
chemical_list: D002352:Carrier Proteins; D014867:Water; D012964:Sodium