An application for visualization of biopolymers. This application can visualize biopolymers by using its original command line and graphical user interface, more than 600 settings for visualization, and more than 20 visualization schemes. This application also supports more than 30 file formats such as PDB and multi-SDF, and can utilize sophisticated visualization methods such as the ray tracing.
An open-source application for ab initio quantum chemical calculation. This application performs electronic structure calculation of molecules by the Hartree-Fock, density functional, many-body perturbation, configuration interaction theories, and so on. Even though this application is freeware, it succeeds in maintaining high-quality and high-performance codes by active development, and has a number of world-wide users. It histrically shares core programs with GAMESS-UK.
An open-source application for visualization of atoms and molecules developed for molecular dynamics. This application supports a number of input file formats for molecular configration, and can perform visualization of three-dimensional atom configration as well as creation of a animation. The main feature of this application is that various useful analysis tools can be used by intuitive control of a graphical user interface (GUI).
A collection of shell scripts for installing open-source applications and tools for computational materials science to macOS, Linux PC, cluster workstations, and major supercomputer systems in Japan. Major applications are preinstalled to the nation-wide joint-use supercomputer system at Institute for Solid State Physics, University of Tokyo by using MateriApps Installer.
An application for first-principles calculation by the joint-DFT method based on a plane-wave basis. By implementation of the joint-DFT method, this application realizes a good convergence for electronic state calculation of molecules in liquid, particular for charged systems. This application is written by C++11, and supports GPU calculation by CUDA. This application also supports diffusive Monte Carlo simulation in cooperation with CASINO.
An open-source application for quantum chemical calculation. This application can perform quantum chemical calculation based on the Hartree-Fock method and the density functional method. The code is developed on the emphasis of readability and flexibility, and can be called from Python scripts. Quantum chemical calculation based on two-electron wave functions (geminals) is also possible.
An open-source application of semi-empirical/ab-initio quantum chemical calculation that comes under an academic license. It performs various quantum chemical calculations based on Hartree-Fock theory, density functional theory, and configuration interaction theory, yielding electronic states and enabling structure optimization and molecular spectrum analysis. Molecular dynamics calculation based on the QM/MM method is also possible by using this software in combination with GROMACS.
An open-source application for first-principles calculation based on pseudopotential and wavelet basis. Electronic state calculation of massive systems is performed with high accuracy and high efficiency by using adaptive mesh. Parallel computing by MPI, OpenMP, and GPU is also supported.
An open-source application for quantum chemical calculation. This package implements various methods for quantum chemical calculation such as Hartree-Fock approximation, density functional theory, coupled-cluster method, and CI (configuration interaction) method. The package is written in C++, and provides API for Python, by which users can perform for preparation of setting and execution of calculation.
ERmod is software for calculating the free energy in soft, molecular aggregate. This program rapidly and accurately calculates the free energy of binding of a molecule in the aggregate through combination of the molecular dynamics simulation and the energy-representation theory of solvation. The solubility of a molecule can be determined with ERmod in arbitrary solvent including supercritical fluid and ionic liquid. Assessment is also possible for the binding strength and site of a molecule in micelle, lipid membrane or protein.