This paper concerns two algorithms designed for acceleration of molecular dynamics simulations using the fast multipole method (FMM) and special-purpose machine (MD-Engine II) for calculating pair interactions. One algorithm is based on a three-dimensional cyclic buffer, which enables efficient cooperation between FMM and MD-Engine II. The algorithm is implemented as part of the particle-processor of MD-Engine II. The processor specifically extracts a set of particles which are contained in nearby regions defined in FMM. The other algorithm is based on a recursive bisection for static load-balancing technique. The efficacy of these algorithms was confirmed by numerical tests.

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A molecular dynamics simulation of the supercritical water was performed on a wide range of temperature and pressure near and above the critical point. Density fluctuations along the critical isochore line at 0.3 g·cm^-3 and some isobaric curves were calculated by the bin analysis method. The obtained values of the density fluctuation were plotted on a P-T phase diagram as contour lines. From this figure, it was found that the density fluctuation has a maximum at the critical point and ranging to a little higher temperature region. The ridge of the density fluctuation found by Nishikawa et al was also confirmed in this work and deviates from the critical isochore to lower density region with increasing pressure. It also found that the density fluctuation occurred not only near the critical point but in a rather wide T-P region of the supercritical state.

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Argon microcluster constituted by 8 molecules was calculated to investigate phase transition from cohesive phase to vapor phase by the molecular dynamics method ("MD method"). The microcluster was calculated under various setting conditions such as changing career gas number and pressure in order to find the optimal setup for observing the phase transition. Then various thermodynamics quantities (internal energy, enthalpy, heat capacity, entropy and free energy) were obtained under the optimal setup conditions. And the calculation results of MD were compared to the results of the Monte Carlo method ("MC method") in order to examine the suitability of the setting condition of MD method, reliability of the obtained thermodynamic quantity and accuracy of leading procedure from internal energy to free energy.

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DFT calculations of the intra molecular site exchange process in square pyramidal five coordinate complexes, [PtX(hfac)₂]^- (hfac = 1, 1, 1, 5, 5, 5-hexafluoro-2, 4-pentanedionate, X = Cl, Br, I), were performed. The calculation reproduces well the X-ray molecular structures and the trigonal bipyramidal transition state energies of three possible paths, two of which actually seem to function, show that the order of the trans effect of halide ligands is Cl < Br < I, and that of the cis effect is Cl > Br > I, which is in accordance with the experimental results.

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The authors have started the design and programming for Summy (Solutions Utilities for Material Mining by Yourself), which is a bench side computing environment for computer-aided material design. Though databases and/or computational facilities for material design are usually located far from bench side, based on a network computing infrastructure using a Grid technology: Ninf, Summy provides access to data base and computers from bench side to get properties rapidly. Using the property estimation function of Summy, material designers can calculate not only molecular orbitals but also many thermophysical properties at their bench side.
Design concept, user interface, and implementation ideas of Summy are overviewed in this article.

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We report the implementation of an atomistic Brownian dynamics simulation of proteins. A protein was described by united-atom model with AMBER91 force field. The solvent was treated by distance-dependent dielectric/surface area model. The computation time of the Brownian dynamics and the calculated results on structure and dynamics of 28-mer ββα fold peptide with the implicit solvent model were compared with those of molecular dynamics simulation with explicit solvent. The Brownian dynamics simulation was 53 times faster than molecular dynamics simulation with explicit solvent. The simulation was stable and the artifacts often observed in simulations at vacuum condition were reduced. The results indicate that the Brownian dynamics with the implicit solvent model can be widely used in studies of protein dynamics by long time simulation in future.

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