Molecular dynamics are performed on systems of two-dimensional periodicity composed of 64 ionic dioctadecyldimethylammonium chloride amphiphiles arranged in a monolayer at 298 K with surface coverages ranging from 57 A2 per amphiphile to 150 A2 per amphiphile. Bond lengths are constrained whereas valence and torsional angles interactions are described by conventional expressions. Nonbonded interactions are introduced through an anisotropic united atom method due to Toxvaerd. The amphiphiles adhere to the surface through electrostatic and nonbonded interactions between the amphiphiles and an underlying substrate. Results are presented for the density normal to the monolayer plane, order parameters, and conformational transition rates. The structure of the two-dimensional layer at the lowest headgroup area studied is quite disordered. Small islands of empty surface surrounded by amphiphiles are formed. As the headgroup area increases, we observed further translational disordering and an increase in the number of amphiphiles aligned with the surface. The g+g+tg+g+ defect observed in one of the chains is stable on a timescale of 250 ps. The equilibrium structures of the two chains are quite different but the conformational dynamics as observed by the transition rates are almost indistinguishable.
SUMMARYThis is the first of a series of papers on the Genesis distributed-memory benchmarks, which were developed under the European ESPRIT research program. The benchmarks provide a standard reference Fortran77 uniprocessor version, a distributed memory MIMD version, and in some cascs a Fortran90 vcrsion suitable for SIMD computers. The problems selected all have a scientific origin (mostly from physics or theoretical chemistry), and range from synthetic code fragments dcsigncd to mcasurc the basic hardware properties of the computer (especially communication and synchronisation overheads), through commonly used library submutines, to full application codes. This first paper defines the methodology to be used to analyse the benchmark results, and gives an example of a fully analysed application benchmark from General Relativity (CR1). First, suitable absolute performance metrics are carefully defined, then thc pcrformance analysis treats the execution time and absolute pcrformance as functions of at least two variables, namely the problem size and the number of proecssors. The theoretical predictions are compared with, or fitted to, the measured results, and then used to predict (with due caution) how the performance might scale for larger problems and more processors than were actually available during the benchmarking. Benchmark measurements are given primarily for the Geman SUPRENUM computer, but also for the IBM 30835, Convcx C210 and a Parsys Supernode with 32 T800-20 transputers.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.