Simulation of interfacial systems with isotropic periodical sum

COMP 12

Xiongwu Wu, WuXW@nhlbi.nih.gov1, Jeffery B. Klauda, klauda@helix.nih.gov2, Richard W Pastor, pastorr@nhlbi.nih.gov3, and Bernard R. Brooks, brb@nih.gov1. (1) Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-8104, (2) Laboratory of Computational Biology, National Institutes of Health, NHLBI, 50 South Dr, Bldg. 50, Room 3308, Bethesda, MD 20892, (3) NHLBI/Lab of Computational Biology, National Institutes of Health, 50 South Drive, Bld 50, Rm 3518, Bethesda, MD 20892
Isotropic periodic sum (IPS) is a method for the calculation of long-range interactions in molecular simulation. The concept of the IPS method is using isotropic distributed images of a local region around each particle to represent remote environment to calculate long-range interactions beyond the local region. The difference between the IPS method and Lattice sum methods like Ewald summation lies in the shape and distribution of remote images for long-range interaction calculation. The isotropic and periodic distribution of IPS images makes the calculation more efficient than lattice sum methods and avoids the symmetry effect introduces from the underlying lattice structures. This work extends the IPS method to interfacial simulation systems which is typically isotropic in two dimensions and periodic in the third dimension. This method describes an interfacial system as a two dimensional (2D) isotropic periodic system on two dimensions and a one dimensional (1D) isotropic periodic system along the third dimension, therefore, is termed as 2+1D IPS. We examined the surface tensions, electrostatic dipolar potentials, as well as density distribution of monolayer and bilayer systems as compared with Ewald summation, 3D IPS, 2D IPS, and cutoff methods. The 2+1D IPS shows little dependence on cutoff distances in simulation properties and reproduces electrostatic-related properties with Ewald summation.
 

Molecular Mechanics
8:30 AM-11:40 AM, Sunday, August 19, 2007 BCEC -- 161, Oral

Division of Computers in Chemistry

The 234th ACS National Meeting, Boston, MA, August 19-23, 2007