Masaaki Kawata

Replica-exchange Monte Carlo method for the isobaric–isothermal ensemble

Abstract We propose an extension of replica-exchange Monte Carlo method for canonical ensemble to isothermal–isobaric ensemble as an effective method to search for stable states quickly and widely in complex configuration space. We investigated the efficiency of the new method on a benchmark testing system which consists of 256 Lennard-Jones particles. The new method enables us to shorten dramatically the relaxation time of phase change from liquid structure to crystal structure in comparison with the conventional Monte Carlo method.

Particle mesh Ewald method for three-dimensional systems with two-dimensional periodicity

Abstract A particle mesh Ewald method for calculating Coulomb interactions in three-dimensional (3D) systems with two-dimensional (2D) periodicity was developed. Computational efficiency and accuracy of this method were evaluated for a TIP3P water system with 2928 particles in a cubic box with 2D periodicity. The accuracy of this method for calculating Coulomb interactions is comparable to our previous method that uses Fourier integral. For calculations with maximum errors in the Coulomb force of 0.4– 20.0 kJ mol −1 nm −1 , the current method was up to five times faster than the previous method.

Rapid calculation of two-dimensional Ewald summation

A computationally efficient method was developed to implement the Ewald summation in calculations for Coulomb interactions in three-dimensional (3D) systems with two-dimensional (2D) periodicity. The computational efficiency and accuracy of this method was evaluated for water systems enclosed in various rectangular parallelepiped boxes (cube, quadratic prism, and slab) and with 2D periodicity. Compared with existing computational methods, this method showed a significant reduction in computational time for all systems examined and was sufficiently accurate for calculating the Coulomb interactions in 3D systems with 2D periodicity, independent of the shape of the simulation box.

Theoretical study for the basicities of methylamines in aqueous solution: A RISM-SCF calculation of solvation thermodynamics

Abstract An ab initio quantum chemical calculation combined with the extended reference interaction site method in statistical mechanics of molecular liquids (the RISM-SCF method) is used to examine the basicities of methylamines in aqueous solution. Free energy changes upon protonation are calculated for a series of methylamines in the gas phase and in aqueous solution, respectively. The gas phase results show a monotonical increase in the basicity with successive methyl substitutions in accord with experiment and earlier theoretical studies. In aqueous solution, however, the results show an irregular order in basicity, which is in qualitative agreement with well established experimental data. Several contributions to free energy changes such as those resulting from solvation and from substitutions are analyzed entirely from a microscopic point of view. It is shown that solvation free energies play an essential role in the determination of the basicity in the solution. Further, it is shown that the solvation structures and the solute electronic structures are altered by the self-consistent treatment in the determination of solute-solvent interactions and that such alterations cause substantial effects on the basicity.

The solvent effect on the acidities of haloacetic acids in aqueous solution. A RISM-SCF study

Abstract The acidities of acetic, fluoracetic and chloroacetic acids in aqueous solution are calculated by means of the ab initio method combined with the reference interaction site method in the statistical mechanics of molecular liquids (the RISM-SCF method). The inversion in the order of acidities experimentally observed when a series of haloacetic acids is immersed into aqueous solution is reproduced. It is shown that the inversion is caused by competition between substitution and solvation effects. The solvation effect is discussed in molecular detail in terms of the charge distribution of the solute and the solute-solvent radial distribution functions.

Acceleration of the canonical molecular dynamics simulation by the particle mesh Ewald method combined with the multiple time-step integrator algorithm

Abstract The canonical molecular dynamics (MD) simulation was accelerated by the integrated method of the multiple time-step integrator algorithm combined with the particle mesh Ewald method (PMEM) applied not only to the calculation of the Coulomb interaction but also of the Van der Waals interaction. Although the previous integrated method, in which the PMEM was used in the calculation only for the Coulomb interaction, yielded a significant acceleration of the MD simulation, a further acceleration by a factor of about 2 in the entire MD simulation was obtained by extension of the integrated method to the Van der Waals interaction.

Acceleration of canonical molecular dynamics simulations using macroscopic expansion of the fast multipole method combined with the multiple timestep integrator algorithm

A canonical molecular dynamics (MD) simulation was accelerated by using an efficient implementation of the multiple timestep integrator algorithm combined with the periodic fast multiple method (MEFMM) for both Coulombic and van der Waals interactions. Although a significant reduction in computational cost has been obtained previously by using the integrated method, in which the MEFMM was used only to calculate Coulombic interactions (Kawata, M., and Mikami, M., 2000, 98, J. Comput. Chem., in press), the extension of this method to include van der Waals interactions yielded further acceleration of the overall MD calculation by a factor of about two. Compared with conventional methods, such as the velocity-Verlet algorithm combined with the Ewald method (timestep of 0.25 fs), the speedup by using the extended integrated method amounted to a factor of 500 for a 100 ps simulation. Therefore, the extended method reduces substantially the computational effort of large scale MD simulations.