A domain decomposition molecular dynamics program for the simulation of flexible molecules with an arbitrary topology of Lennard-Jones and/or Gay-Berne sites.

Abstract

We describe a new parallel molecular dynamics program GBMOLDD which uses the domain decomposition algorithm. The program is designed to simulate molecular systems composed of both spherically-symmetric and anisotropic sites connected via arbitrary topology and described by standard force fields. The program is oriented mainly towards simulations of liquid crystalline systems including mixtures of mesogenic molecules and mesogens confined in host media. Benchmark results are presented for a model liquid crystal dimer composed of two mesogenic units linked via a flexible alkyl chain. The benchmarks compare favorably to those obtained via a parallel replicated data algorithm.